Syria and Russia have come to an agreement reorganizing Moscow’s military presence in the country after more than a year and a half of negotiations, the Syrian foreign ministry announced on Sunday.

The announcement described the agreement as the most significant development since negotiations with Russia began after rebels overthrew the dictator Bashar al-Assad in late 2024, adding that it opens the way for a new phase in relations between the two countries.

Russia long maintained a military presence in Syria, dating to the Soviet era. It included two air bases and a naval port on the Mediterranean Sea. They provided Russia with its only supply and stopover hub in the eastern Mediterranean for planes and ships traveling to and from Africa.

But that presence, along with Moscow’s strategic relationship with the Syrian government, was thrown into doubt after rebels overthrew Mr. al-Assad. Russia had backed the Assad regime throughout the nearly 14-year civil war against an array of rebel groups, and regularly carried out deadly airstrikes on rebel-held territory.

Soon after taking office, the new Syrian president, Ahmed al-Sharaa, said he was not in a hurry to expel Russia from Syria, noting that Russia had supplied Syria’s military with weapons for decades.

Russia once controlled the naval base at the Mediterranean port of Tartus. But after the ouster of the Assad regime, it was limited to using a single berth when the Syrians allowed it.

The Syrian government also canceled Russia’s contract to manage the Tartus port and signed a deal with Dubai Ports World, which agreed to invest $800 million in the facility.

The Syrian foreign ministry announcement on Sunday said the two countries had reached a memorandum of understanding that outlines a reorganized Russia’s presence on the Syrian coast, at the Hmeimim Air Base outside the city of Latakia and at the Tartus naval port, according to state media.

Civilian facilities will be transferred to Syrian government management and gradually integrated into the country’s civilian administration, and Russian military bases will be turned into joint training centers, according to the ministry.

It said the new arrangements were aimed at safeguarding the interests of both countries and sets a deadline of no more than three months to complete the transition.

Russian state media did not immediately report on the agreement and much remains to be decided.

Previously, Mr. al-Sharaa has said that any new relations with Russia “must address past mistakes” and called for compensation for the destruction Russia had caused during the war.

Mr. al-Sharaa’s government has also called for Russia to hand over Mr. al-Assad, who received asylum in Russia after he fled Syria as the rebels closed in on Damascus in December 2024.