In the eighteenth and nineteenth centuries, the southern city of Mogadishu became Somalia's most important city. Mogadishu, Merca, and Baraawe, had been major Somali coastal towns in medieval times. Their origins are unknown, but by the fourteenth century travelers were mentioning the three towns more and more as important centers of urban ease and learning. Mogadishu, the largest and most prosperous, dates back at least to the ninth century, when Persian and Arabian immigrants intermingled with Somali elements to produce a distinctive hybrid culture. The meaning of Mogadishu's name is uncertain. Some render it as a Somali version of the Arabic "maqad shah," or "imperial seat of the shah," thus hinting at a Persian role in the city's founding. Others consider it a Somali mispronunciation of the Swahili "mwyu wa" (last northern city), raising the possibility of its being the northernmost of the chain of Swahili city-states on the East African coast. Whatever its origin, Mogadishu was at the zenith of its prosperity when the well-known Arab traveler Ibn Batuta appeared on the Somali coast in 1331. Ibn Batuta describes "Maqdashu" as "an exceedingly large city" with merchants who exported to Egypt and elsewhere the excellent cloth made in the city.

Through commerce, proselytization, and political influence, Mogadishu and other coastal commercial towns influenced the Banaadir hinterlands (the rural areas outlying Mogadishu) in the fifteenth and sixteenth centuries. Evidence of that influence was the increasing Islamization of the interior by sufis (Muslim mystics) who emigrated upcountry, where they settled among the nomads, married local women, and brought Islam to temper the random violence of the inhabitants.

By the end of the sixteenth century, the locus of intercommunication shifted upland to the well-watered region between the Shabeelle and Jubba rivers. Evidence of the shift of initiative from the coast to the interior may be found in the rise between 1550 and 1650 of the Ujuuraan (also seen as Ajuuraan) state, which prospered on the lower reaches of the interriverine region under the clan of the Gareen. The considerable power of the Ujuuraan state was not diminished until the Portuguese penetration of the East African coast in the seventeenth and eighteenth centuries. Among Somali towns and cities, only Mogadishu successfully resisted the repeated depredations of the Portuguese.