The phylogenetic data of the Java eel population is crucial for future catadromous aquaculture in Indonesia. The study aims to know how eel species from Java and West India differ in their evolutionary patterns. Four river estuaries in Central Java and one estuary in West Java, Indonesia, were chosen as samples of Javanese eel origins. Phylogenic comparison data from five regions of the Western Indian Ocean and one region of the Philippines (Pacific Ocean) were examined, taken from GenBank® data. The results showed that BLAST from 25 eels from Central and West Java was Anguilla bicolor bicolor (homology value 96 – 100%). The phylogenetic tree revealed that samples from Java nested into the West Indian Ocean with two Clades but were isolated from the Pacific Ocean eels. There are 25 pairs of monophyletic samples estimated to be the most recent common ancestor among the Indian Ocean eel samples from west to west, east to east, and west to east.