Raja Ampat Regency is a regency of Southwest Papua Province of Indonesia. The regency, which was formed by separating the archipelago from Sorong Regency, based on the Law 26 of 2002, was inaugurated on 12 April 2003. It consists of a number of groups of islands situated off the north-west end of West Papua; the four main islands from south to north are Misool, Salawati, Batanta, and Waigeo, but there are thousands of smaller islands and islets. At present, the regency covers a land area of 7,559.61 km², with a total area (including 59,820.01 km² of sea area) stated as 67,379.61 km². It had a population of 42,508 at the 2010 Census and 64,141 at the 2020 Census; the official estimate as at mid 2025 was 74,965 (comprising 38,979 males and 35,986 females). The principal town lies at Waisai on Waigeo Island.

On 25 October 2013 the People's Representative Council (DPR) began reviewing draft laws on the establishment of new regencies, including two new regencies of North Raja Ampat and South Raja Ampat within the borders of the existing Raja Ampat Regency. As at May 2024, these changes have not yet been implemented.

Raja Ampat is known for its beautiful sea and scenery. It is recognized as the home of the largest coral reef biodiversity in the world. With more than 550 distinct variety of coral, 700 different kinds of mollusks, and 1427 different species of fish, it is a significant center for marine biodiversity. Seventy-five percent of all known coral species may be found in the seas around the Raja Ampat Islands, which are home to some of the world's most diverse species. Under the Terumbu Karang Sehat Indonesia programme, Konservasi Indonesia supported the development of a tourism spatial plan for Raja Ampat Regency and drafted provisions for a local tourism-management regulation.

Raja Ampat Regency is a regency located at a position of 2° 25' north latitude to 40° 25' latitude south, and 130° – 132° 55' east longitude. Administratively, the boundaries of the Raja Ampat Regency are as follows:

At the 2010 Census, the regency was divided into seventeen districts (kecamatan). Subsequently, seven additional districts have been created by the division of existing districts. The twenty-four districts are tabulated below with their areas and their populations at the 2010 Census and the 2020 Census, together with the official estimates as at mid 2025. They are grouped according to the proposed split into three regencies currently under consideration (since 2013) by the government, but postponed due to the government moratorium on the creation of new regencies. The table also includes the locations of the district administrative centres, the number of administrative villages in each district (4 urban kelurahan in Waisai Town District, and 114 rural kampung in all the other districts), the number of named islands in each district, and its postal code.

Note: (a) not to be confused with the similarly named Salawati Tengah District within Sorong Regency.
(b) the Ayau Islands (including Ayau District) lie some distance to the north of Waigeo.

Since 2010, the new Waisai district has been created from part of Waigeo Selatan District, the new Tiplol Mayalibit District has been created from part of Teluk Mayalibit District, the new Supnin District has been created from part of Waigeo Utara District, and the new Ayau District has been created from part of Kepulauan Ayau District.

Misool and Kofiau Islands (comprising the first six districts listed above) are currently under Indonesian government consideration to be split off to form a separate South Raja Ampat Regency under proposals approved in 2014 by the Indonesian Parliament. Similarly, Waigeo and its surrounding small islands (comprising the last thirteen districts listed above) are currently under Indonesian government consideration to be split off to form a separate North Raja Ampat Regency under proposals approved in 2014 by the Indonesian Parliament. However, as at 2024, these changes have not yet been implemented.