Yes but the conflict was mainly between Portugal and the Sultanate of Oman, who ran all kinds of businesses and trade along the eastern Africa coast from Mozambique all the way to Somalia (the south). It's main commodity was slave trade. The Portuguese also involved in slave trade to meet demands in the Americas came to the region.Revolutionary wrote: Have Ajuuran ever confront the Portuguese empire? According to the map, they're neighbors.
Somalia/Ajuran aided the Omanis but they were not the leaders of the conflict. Back then Sultanate of Oman was quiet a power.
In the South the Omanis and Ajuran on one sided combated with the Portuguese and the Gallas (Oromo) on separate fronts.
In the north (Djibouti, Somaliland and parts of Somali Region), the locals under Adal/Ifat Islamic Empire combated the Christian Abyssinia.
There were as many Muslim Habesha on Adal side as Somalis. There was no nationalism or ethnicity back then. The two Somalis of north and south had no direct political or economic contacts. There was no south role in the wars against Abyssinia but Siad Barre tried to add that to their factious history.
After the wars, many Habesha Muslims who fought for Adal, decided to stay on the land while Afar, Somalis and others had returned to their original regions.
That continued well into until 1960 when SL and Somalia briefly merged to form Somali Republic, which later was renamed The Somali Democratic Republic under the Revolutionary Council of Maj. General Mohamed Siad Barre. That was the only time the two ever had a union and it was short lived.
This explains the social and attitude difference in the two as well as cultural. It is no different than Eritrea and Ethiopia.