Abstract : Information on AnGR that include genetic diversity and phylogenetic relationships between breeds or populations are important in animal conservation and breeding programs. This study aimed to identify microsatellite diversity and phylogenetic relationships of seven Indonesian swamp buffaloes. A total 72 of DNA samples from seven different populations were used in this study. The observed microsatellite marker consists of CSSM047, ILSTS011, and BM1706. The results showed that the genetic diversity of seven Indonesian swamp buffaloes populations in this study was relatively high, with Ho values ranging from 0.4306 (ILSTS011) to 0.6111 (BM1706). All microsatellite loci used were polymorphic. These phylogenetic relationships of seven Indonesian swamp buffaloes populations were grouped into two main clusters. The first cluster consists of Banten, West Nusa Tenggara, North Toraja, Konawe, and Kolaka populations, while the second cluster consists of Bombana Islands and the Bombana mainland populations. The genetic diversity of seven Indonesian swamp buffaloes populations in this study was relatively high, with Ho values ranging from 0.4306 to 0.6111. All investigated microsatellite loci were polymorphic. These phylogenetic relationships of seven Indonesian swamp buffaloes populations were grouped into two main clusters. The first cluster consists of Banten, West Nusa Tenggara, North Toraja, Konawe, and Kolaka populations, while the second cluster consists of Bombana Islands and the Bombana mainland populations. This result very useful in conservation and breeding programs for Indonesian swamp buffalo.