Pasundan cattle is one of the native Indonesian species and molecular data is needed to further generate historical and ancestral information about cattle breeds. Therefore, to understand the maternal inheritance and phylogeny of Pasundan cattle, the nucleotide sequence of the D-loop region was analyzed. The DNA samples were collected from the Research Center for Biotechnology, BRIN, Cibinong, Indonesia. The phylogenetic tree reconstruction was analyzed using the Neighbor-joining method based on Kimura 2 Parameters. Based on the phylogenetic analysis, the Pasundan cattle showed two clusters, namely Bos indicus and Bos javanicus CERZA. Furthermore, the result showed that they originated from two maternal lineages and native cattle in Indonesia, including Madura cattle.