Phylogenetic analyses on the Phylum Mollusks has so far been conducted by many researchers in the world. However, there was no report on taxonomic analysis on Acila divaricata vigila which is belonging to Class Bivalvia, Subclass Protobranchia. In this study, we performed molecular phylogenetic analysis on Acila divaricata vigila using 16S rRNA sequence through maximum likelihood method. As a result, it is clearly divided into the legion of mollusk classification unit (when you zoom in order) and represented to support the current classification in the Phylum Mollusca belong to Class Bivalvia, Subclass Protobranchia, Subclass Pteriomorphia, Subclass Paleoheterodonta, Subclass Heterodonta and Subclass Anomalodesmacea. To our knowledge, this is the first report of molecular phylogenetic analysis on Acila divaricata vigila using 16S rRNA gene and these data suggests that 16S rRNA gene will be useful for analyzing the phylogenetic relationship of Subclass Protobranchia.