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Masheer is Indonesias endangered local fish. This study conducted to characterize and mapping the phylogenetic relationship of Masheer fish from East Java, West Kalimantan, Padang and North Sumatra using a partial sequence of mtDNA 16S rRNA. PCR amplicons at 542 bp in length. The construction of phylogenetic topology was made based on ML and NJ method using Kimura-2 parameter model. Based on the phylogenetic topology showed that Tor fish from Pasuruan are closely related to Tor duoronensis from Padang with a bootstrap value of 66%, while Tor duoronensis fish from North Sumatra and Tor tambra from West Kalimantan are in separated clusters. Sequence was compared and multiple sequence alignment revealed some polymorphic sites which can be used to differentiate Genus Tor from Indonesia. This 16S rRNA gene finding has a significant contribution to indicate phylogenetic of Masheers fish in Indoensia