[3][4] After Hayreddin's death, the province remained the domain of the Kapudan Pasha, the new title of the commander-in-chief of the navy, a position of great power and prestige: its holder was a vizier of three horsetails and a member of the Imperial Council.

[3] Although the Kapudan Pashas resided in the Imperial Arsenal, Gallipoli remained the official capital (pasha-sanjak) until the 18th century.

Under Merzifonlu Kara Mustafa Pasha, the sanjaks of Mezistre and Karli-eli were detached and incorporated in the new Eyalet of the Morea.

[3] From 1701–1821, the office of the Dragoman of the Fleet, entrusted to a Phanariote Greek, served as intermediary between the Kapudan Pasha and the autonomous communities of the Aegean islands.

By the early 19th century, the eyalet was reduced to the sanjaks of Biga (now the pasha-sanjak, its centre was moved to Kale-i Sultaniye in 1855), Gelibolu, Rodos, Sakız, Midilli, Limni (Lemnos) and Cyprus.