In an interview with a local TV station, Hassan Sheikh Mohamud said Israel’s recognition of Somalliland marked one of the darkest days in Somalia’s history.
He said Mogadishu remained committed to peace in its pursuit of reunification.
Israel recognized the breakaway region of Somaliland as an independent state in late December 2025, becoming the first country to do so.
But Mogadishu maintains that the recognition is null and void.
In Somaliland too, some are opposed to ties with Israel, citing atrocities in Gaza and the occupation of several Muslim countries.
Dozens have been arrested for protesting against the alliance, including religious scholars and youths waving Palestinian flags.
Somaliland’s value as a strategic military and trade hub on the Gulf of Aden, close to Yemen, is coveted by Israel which has long sought a naval presence on the Red Sea Coast.
The Somali president’s remarks come after days of violent clashes in the capital Mogadishu, prompted by an extension of his mandate by a year.