The first city belonging to the Islamic civilization was Medina, where the prophet Mohammed moved to in 622 AD, known as Year One in the Islamic calendar (Anno Hegira).
In addition to a wealth of Arabic historical data, Islamic cities are recognized by Arabic inscriptions, architectural details and references to the Five Pillars of Islam: an absolute belief in one and only one god (called monotheism); a ritual prayer to be said five times each day while you are facing the direction of Mecca; a dietary fast at Ramadan; a tithe, in which each individual must give between 2.5-10% of one's wealth to be given to the poor; and hajj, a ritual pilgrimage to Mecca at least once in his or her lifetime.
This interesting site is in Mali, on what was the camel caravan crossing the Sahara desert and connecting West Africa with Libya, Tunisia, and the rest of North Africa with the wider world of the Mediterranean Sea, beginning in the 11th century AD. Occupied by Berbers and Tuareg nomads, Tadmakka was known throughout the Arab world as a city that "resembled Mecca the most".
The modern city of Samarra was an important Islamic center on the Tigris River during the Abbasid period. Samarra was founded in AD 836 by the Abbasid dynasty caliph al-Mu'tasim [ruled 833-842] who moved his capital there from Baghdad.
Timbuktu (also spelled Tombouctou or Timbuctoo) is on the inner delta of the Niger River in Mali, where, Arabic history tells us, it was founded about AD 1100 as a seasonal camp herders. Timbuktu's location on a camel route between the coast and salt mines made it a significant node on the the trade network of gold, salt and slavery.
Al-Basra in Morocco was an Islamic civilization center between AD 800-1100, where an Idrisid dynasty mint was established, and a wide variety of manufactured and agricultural goods were produced.
Old Qandahar, located near the modern city in south central Afghanistan, was probably first occupied before the 6th century BC, the first substantial occupation belongs to the Achaemenids about 520 BC, and it became part of the Islamic empire in 680 AD
Aqaba is a medieval (12th century) Islamic fortress, called Ayla when it was the capital city of the early Islamic period from AD 650 to the arrival of the Crusaders in 1116 AD
Shanga is an archaeological site on an island in the Lamu archipelago off the coast of eastern Africa (ca 750-825). The first buildings at Shanga were a large wood enclosure protecting a well, ceremonial buildings and craft workshops; outside the wall was a community of small residential structures
Al Rafiqa is an Abbasid site located in what is today in Syria; its buildings constructed by Caliph Al-Mansur in 722 AD, include a complex of palaces enclosed by a massive horse-shoe shaped wall
Hamdallahi was the capital city of the late Islamic Fulani caliphate of Macina (or Massina or Masina), It's fortified city buildings were constructed in 1820 and destroyed in 1862.