The Governorate of Chiloé was political and military subdivision of the Spanish Empire that existed, with a 1784–1789 interregnum, from the 1600s to 1826. The Governorate of Chiloé depended on the Captaincy General of Chile until the late 18th century when it was made depend directly on the Viceroyalty of Peru. The administrative change was done simultaneously as the capital of the archipelago was moved from Castro to Ancud in 1768. The last Royal Governor of Chiloé, Antonio de Quintanilla, depended directly on the central government in Madrid.

The Governorate of Chiloé had its de jure northern limit a Bueno River in continental Chile. There the governorate limited with the territories of Valdivia. The area de facto controlled included the Chiloé Archipelago, the seashore forts and settlements north of Chacao Channel plus the Mission of Nahuel Huapi which was nevertheless financed from Valdivia. Historian Gabriel Guarda do however disagree claiming the Mission of Nahuel Huapi was within the jurisdiction of Valdivia. The so-called juncos of Osorno (Huilliches) attempted in the late 18th century to have their lands, that lied just south of Bueno River, to be removed from the Governorate of Chiloé and incorporated to Valdivia. The reason of this was their bad relation and history of warfare with the settlements of around Chacao Channel.

All 17th century Royal Governors were named by the Royal Governor of Chile. In the 18th century this system changed and while still named by the Royal Governor of Chile the position were to be ratified by the King of Spain. Later in the 18th century the Viceroy of Peru took over the duties of naming governors but still with the need of ratification by the King of Spain. Formally the office was granted based on merits during all of the 17th century. However, in the early 18th century "pecuniary service" begun also to be considered, which meant in practice that the office could be purchased. This practice was abolished in 1750. The office of Governor of Chiloé was commonly used to booster a carrier and then access more desirable positions of power in Central Chile.

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