The Kutubiyya Mosque that stands in Marrakech today is actually the second of two very similar Kutubiyya mosques that were built on the same site by the Almohad ruler Abd-al-Mu'min in the twelfth century. While there are no exact dates available for the periods of construction of the two mosques, the sequence of events has been loosely reconstructed based on contemporary texts. After capturing the city of Marrakech in the wake of the death of Almoravid leader Ali bin Yusuf in 1147/541 AH, Abd-al-Mu'min built the first Kutubiyya mosque on the site of Ali bin Yusuf's former palace in the southwest quarter of the medina. Construction of the first Kutubiyya mosque began in the years between 1147/541 and 1154/548 AH and concluded by 1157. The second mosque was started after 1154/548 AH, and was at least partially constructed by September 1158/552 AH, when the first prayers were said there. Construction of the second Kutubiyya most likely concluded by 1162/557 AH, although one text writes that it was only fully completed during the reign of Abd-al-Mu'min's grandson Abu Yusuf Ya'qub al-Mansur in 1190/585 AH.

The early history of the two Kutubuyyia mosques is enigmatic, as it remains uncertain why Abd-al-Mu'min would construct two almost identical mosques on the same site less than a decade apart. Various theories have been proposed to explain Abd-al-Mu'min's motivations for ignoring the Muslim convention of building only one Friday mosque in each city. Some scholars contend that the second mosque was built to correct the inaccurate qibla orientation of the first mosque; however, the second qibla orientation is actually less accurate than the first. Others argue that perhaps Marrakech's growing population merited an expansion of the original Kutubiyya mosque to accommodate more worshipers. A third view attributes the second construction to the desire of Abd-al-Mu'min to commission as many public buildings as he could into order to create an impressive personal legacy as a great builder. No matter what the actual motivation was for the doubling of the original mosque, the second mosque was not built specifically to replace the first mosque, as there was a period of at least thirty years in which two Kutubiyya mosques shared the site. It was only long after the construction of the second Kutubiyya mosque that the first mosque was ruined.

The first Kutubiyya mosque is in the overall form of a rectangle approximately 80 meters wide east to west and 60 meters long north to south. The longitudinal axis of the building is rotated twenty-six degrees counter-clockwise from the north-south meridian to accommodate qibla orientation, though a true orientation toward Mecca would require a counter-clockwise rotation of eighty-nine degrees in plan. The most significant change, and arguably the reason for its construction, was the reorientation of the plan based on a rotation of the qibla wall five degrees counter-clockwise from its original axis. Ironically, this rotation causes the qibla of the second Kutubiyya to point five degrees further away from Mecca than that of the first mosque.

The courtyard was located to the north of the mosque, adjacent to the larger prayer hall at the south. The prayer hall followed the T-shaped plan observed in other mosques constructed by Abd-al-Mu'min, namely the mosque at Taza, the mosque at Tinmal, and the second Kutubiyya. One wide transverse nave ran along the qibla wall at the south of the prayer hall, and from its center three wide central naves extended perpendicularly towards the north along the length of the hall. On either side of the three central naves were seven smaller parallel naves, resulting in seventeen parallel naves in total. The total length of the longitudinal naves was equal to six times the width of the large transverse nave, or approximately 36 meters. The width of the courtyard is equal to the width of the nine central naves, or 45 meters, and its length is equal to four times the width of the transverse nave, or 24 meters. The four outermost naves on each side of the prayer hall extend along the length of the courtyard in order to complete the rectangular shape of the plan. The extensions of these eight naves form annexes on either side of the sahn.

Entry to the mosque was possible via any of the four entrances on each of the east and west walls, of which three opened into the prayer hall directly, and one opened into the courtyard. The east elevation is known to have opened directly onto a street populated with numerous bookshops, which led to the mosque's informal name, "the mosque of the booksellers," from which the current name of Kutubiyya was derived. There was an additional public entry into the sahn on the north wall along the central axis. In the prayer hall, to the left of the mihrab was a private entrance for the imam. There was a second private entrance for the prince that opened into the maqsura.

Entering the mosque through the portal on the north elevation, one would have walked into the sahn on axis with the ablution fountain in the center of the courtyard. Passing through the courtyard along the central axis, one would have then entered the prayer hall along the widened central nave in front of the mihrab niche on the qibla wall. The interior of the prayer hall was a typical hypostyle hall in which over a hundred columns supporting horseshoes arcades touched down along the axes of the parallel naves. This immense hall would have been able to hold 20,000 worshippers.

The mosque was built primarily in brick, which formed all of its columns, all of its arcades, the center of the qibla wall, and the mihrab niche. The exterior walls to the south, east, and west were constructed of sandstone, and the north wall was originally a portion of the stone wall of the Almoravid fortress which it abutted. The building itself was likely sparsely ornamented, according to the Almohad tradition. However, it did contain several architectural features that are known to have been spectacularly decorated.

Two of the most notable architectural elements of the first Kutubiyya mosque were its famous retractable maqsura and minbar, both designed by engineer al-Hajj Ya'ish of Malaga. After the imam entered the prayer hall via his private entry to the left of the mihrab, he would activate an elaborate mechanical system based on counterweights and pulleys as he walked towards the niche of the mihrab. His weight on the path to the mihrab would cause the minbar to move forward into the prayer hall from the enclosure to the right of the mihrab where it was previously housed. There was another similar weight-activated mechanism that would serve to raise and lower the maqsura that separated the area reserved to the prince and his court for private worship. The prince entered the mosque via a private underground corridor that led directly from his palace to the enclosure of the maqsura, and when he entered his worship area, the retractable maqsura would rise up from a ditch in the floor along grooves in the walls to provide privacy. The maqsura was a carved wooden screen two meters tall, and according to legend it enclosed a space large enough to hold a thousand men. While this description is now thought to be an exaggeration, the scale and visual power of the maqsura was certainly immense and intimidating.

There was also a room in the first Kutubiyya mosque reserved for the special display of the famous Koran of Cordoba, acquired by Abd-al-Mu'min in 1157 from the Cordobans and prized by the rulers of the Almohad dynasty. This room, which contained other significant Korans as well, was luxuriously appointed with precious stones and enamels, and its entries were regulated by mechanized openings.

The minbar that was seen in the first Kutubiyya mosque was originally located in the first mosque of Ali bin Yusuf. It is a famous example of the Andalusian decorative arts that were patronized by the Almoravid and Almohad rulers of Morocco. The minbar was moved to the first Kutubiyya after Abd-al-Mu'min closed the Ali bin Yusuf mosque; while the mosque that his predecessor built had to be destroyed to usher in a new dynasty of Almohad rule, Abd-al-Mu'min preserved and reused its beautiful and renowned minbar to glorify his new mosque in Marrakech. This minbar later sat in the second Kutubiyya mosque from the time of its construction until 1962, at which point it was moved to the 'Badi Palace in Marrakech. Extensive studies have been made of the minbar and its intricate decoration, which is well-preserved to this day. Built in a Cordoba workshop as a commission for Almoravid sovereign Ali bin Yusuf, the piece is a masterpiece of eleventh-century Andalusian decorative crafts. The minbar is a wooden structure in the shape of a triangle with a stepped hypotenuse. The piece is 3.5 meters long, 0.9 meters wide, and 3.9 meters tall. Panels along the triangular faces are decorated with intricate wooden carvings and bone inlays of vegetal and geometric motifs. A six-centimeter-wide band of Koranic inscriptions runs along the stepped profile of the triangular faces. The Kufic script is represented in blackwood and bone on a wood marquetry background and is one of the best detailed western Islamic inscriptions. The quality of the craftsmanship of the minbar as a decorative piece is virtually unparalleled.

The minaret of the Kutubiyya mosque was constructed after the erection of the first mosque but before that of the second. The minaret shares the same orientation as the second Kutubiyya, which indicates that it was built after the first qibla orientation had been determined to be faulty. The minaret is grand in scale, with a total height of 77 meters and a square shaft measuring almost 13 meters to a side. The form of the minaret is typical of the Almohad style, where a large square shaft rises up to approximately four-fifths of the height of the tower, at which point stepped merlons cap the perimeter of the shaft. Ramps inside the minaret lead up to an outdoor gallery at the level of the merlons. From the center of this level a smaller square shaft, in this minaret seven meters to a side, rises one additional level before it is crowned by a domed lantern and metal finial. The main shaft of the minaret is articulated on each face at four levels with varying combinations of blind arches and arched openings. A wide band of green ceramic tiles rings the minaret directly below the level of the merlons. The body of the minaret is constructed of large sandstone bricks, and the decorative carvings that surround the arched fenestrations are also of sandstone. Comparisons are often made between the Kutubiyya minaret and the Almohad minarets at the Giralda mosque in Seville and the Hassan mosque in Rabat.

The plan of the second Kutubiyya is virtually identical to that of the first, with only a few small modifications. The most significant change, and arguably the reason for its construction, was the reorientation of the plan, based on a shift of the qibla wall 5 degrees further from the north than the orginal qibla orientation. Ironically, this leads the second mosque to face 5 degrees further away from Mecca. The difference in orientations between the two mosques led to the creation of a slim wedge of space between the two buildings that each adjoin the minaret, with the first mosque at its southeast corner and the second mosque at its northeast.

The layout of the second mosque and prayer hall is exactly the same as in the first Kutubiyya, except that each of the parallel longitudinal naves are slightly wider, giving the mosque overall a slightly larger width. Also, only the central longitudinal axis is as wide as the transverse nave, bringing the T-shaped plan more clearly into focus. Domed cupolas along these two widened perpendicular axes of the prayer hall further the definition of the hierarchy among naves.

Just as the second Kutubiyya resembled the first in plan, it was also constructed of the same materials as the first, and with the same decorative strategy. For centuries the minbar from the first Kutubiyya was located in the second Kutubiyya, although it is no longer housed there today. Today the interior of the prayer hall is painted a clean white, and multi-toned rush mats on the floor provide the only color inside.

In the decades that followed its construction, the Kutubiyya mosque in its two incarnations was not only the most important mosque in Marrakech, but further in the entire Almohad empire that stretched from Spain across the Western Mahgreb. However, when in 1195 Abd-al-Mu'min's grandson Abu Yusuf Ya'qub al-Mansur built a new congregational mosque in Marrakech to memorialize his own exploits as a sovereign, the Kutubiyya lost its religious and political power as the seat of the Friday prayers in Marrakech. From that point forward, the mosque and its famous minbar fell into disuse, and at some subsequent point the first Kutubiyya mosque was ruined. Today, while it does not hold the same societal significance that it did upon its construction, the second Kutubiyya mosque remains a well-preserved example of Almohad religious architecture in Marrakech.

The minaret of the mosque suffered minor damage in the September 8 earthquake.

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