The Church of Panagia Mouchliotissa (Παναγία Μουχλιώτισσα), located in the district of Fener, is the only Byzantine church in the city that has continued to function as an Orthodox church. This church, which is also known as St. Mary of the Mongols, was a Middle Byzantine structure significantly altered during the Palaiologan and Ottoman eras. 
The church, originally known as Theotokos Panagiotissa (Θεοτόκος Παναγιώτισσα), served as the katholikon of the convent founded by Maria Palaiologina in the late 13th century. However the church has been significantly altered over time, with its original structure - a tetraconch - dating back to the 11th century. The area located north of the Cistern of Aspar on the slope of the Fifth Hill overlooking the Golden Horn had long history of monasticism, with a convent being established in the area by Sopatra, the daughter of Emperor Maurice (582-602) for the noble woman Eustolia, which Sopatra herself later joined. The tetraconch possibly once belonged to the Monastery of Panagiou known to have been in the immediate vicinity in the 11th century. This monastery, which was associated with the Lavra Monastery in Athos, was probably disbanded after the Fourth Crusade in 1204. The father-in-law of George Akropolites, perhaps Isaak Doukas, uncle of Michael VIII, reestablished a monastery in the area following the recapture of Constantinople in 1261. This monastery, probably Mouchliotissa, was again renovated in 1266-67 when the artist Modestos contributed to its decorative program. 
The next founder was Maria Palaiologina (died c. 1307), an illegitimate daughter of Michael VIII (1261-1282) and half sister of Andronikos II (1282-1328). In 1265, she was sent to be the wife of Khan Hulagu; however as he died before her arrival, she married his son Khan Abaqa. She returned to Constantinople and refounded the convent following the death of Abaqa around 1282. The name of this church, Mouchliotissa, seems to derive the title of Maria Palaiologina, “Lady of the Mongols”. She purchased the monastery, which included the church, a bath, an orchard, and a vineyard, and allocated her entire personal fortune to the convent. The convent also had estates in Thrace that helped sustain the endowment for 33 nuns who were accepted without being required to pay an entrance donation. It seems that she repaired the church, adding a narthex to the existing tetraconch, and perhaps redecorating the church. She eventually retired to this convent, though it is not certain if she took up residence immediately or later in life. 
According to an unreliable tradition, Sultan Mehmet II gave the church to the architect Christodoulos around 1462 as a reward for erecting Fatih Mosque over the site of the Church of the Holy Apostles. A copy of Mehmet II’s firman, which confirms the special status of Mouchliotissa, is now displayed inside the church. Its Turkish name Kanlı Kilise (“Bloody Church”) derives from a supposed final battle between Byzantine and Ottoman forces here on May 29, 1453 when Mehmet II conquered the city. The church served as a parish rather than a monastic church during the Ottoman era. It was severely damaged by fires in 1633, 1640 and 1729. A small girls’ school was attached to the property in the 19th century which was served by five priests. During this period, it was a dependency of the Monastery of Megalon Spelaion in the Peloponnese. The church was vandalized during the anti-Greek riots in 1955, but was restored later that year.
When it was constructed as a monastery in the 11th century, the church was originally a domed tetraconch measuring 12 x 12 meters. It consisted of a central square, with each side opening to opened to semicircular apses. Each of these apses has three smaller niches or apsidoles on the interior. A dome was supported by four columns topped Corinthian capitals (now covered with plaster). Nothing is known about the decoration and positions of its windows, cornices and roof. While the tetraconch is uncommon in Constantinople, another example in the area is the 11th century church of Panagia Kamariotissa on Chalki Island (Turkish Heybeliada). 
A tripartite narthex was probably added during the renovations funded by Maria Palaiologina in the late 13th century. Its current plan is irregular, due to Ottoman-era extensions on its southern and western sides probably made in the eighteenth century perhaps to increase its size in order to house a larger congregation.  As a result, only surviving Byzantine features of the church are the eastern and northern apses, the two northern bays of the narthex, and the dome of the naos. One dome of the original two-domed narthex also survives. There is a staircase leading to underground chambers. One of these is a barrel vaulted room, while the other chamber might have been part of the inner narthex and later served as an hagiasma (holy spring). It might have originally perhaps functioned Palaiologan tomb vaults. The Ottoman-era additions also include an exonarthex and pointed arches, along with its bell tower which was erected in 1892. While the artist Modestos is recorded as decorating the church at the end of the 13th century, the traces of mural paintings existing today are from the post-Byzantine era.