The Military-Political System of Samos (Greek: Στρατοπολιτικόν Σύστημα Σάμου) was a provisional regime that existed in the island of Samos during the Greek War of Independence.

Samos rose up against Ottoman rule on 18 April 1821, under the leadership of Konstantinos Lachanas. In May 1821, the Samiot leader Lykourgos Logothetis formalized the provisional administrative regime of the island, with the promulgation of the "Military-Political Organization of the Island of Samos" (Στρατοπολιτικός Διοργανισμός της Νήσου Σάμου). This constitutional document roganized both the executive-legislative and military administration of the island. At the apex of the system was a Governor-General (Γενικός Διοικητής), assisted by three Political Judges (Πολιτικοί Κριτές) who were elected by a General Assembly of the island, composed of the elected ephors of each village, and the Secretary of the Administration (Γραμματεύς του Διοικητηρίου). There were also a Police President, Harbour Masters and Customs officials. The island's military was organized into four chiliarchies, with the Governor-General as the commander-in-chief. Logothetis appointed four of his closest aides as the first chiliarchs, who appointed subordinate pentakosiarchs, and they in turn appointed subordinate hekatontarchs, etc.

Nevertheless, the Greek provisional government that emerged from the First National Assembly at Epidaurus attempted to abolish the separate Samian institutions with its law on provincial administration 30 April 1822, and impose an appointed governor, Kyriakos Moralis. This led to a short civil war on the island, with the supporters of the local system winning out. With the exception of a short period in 1828–1830, during the governorship of Ioannis Kapodistrias, when Samos was administered as part of the Province of the Eastern Sporades, the island retained its autonomous political system.

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