Abstract Freshwater eels (Anguilla spp.) are catadromous fish with widely distributed in the world and have long spawning migration. Palabuhanratu Bay is one of the potential areas and high activity for freshwater eels fishing. There have several rivers that flow to Palabuhanratu Bay. Species taxonomy certainty is needed to determine resource management. This study aimed to investigate the taxonomic status of Anguilla spp. based on Cytochrome Oxidase subunit I (COI) gene markers in seven rivers that flow to Palabuhanratu Bay. The sample was collected using timber traps (local name is bubu) from August and December 2014. The result of molecular identification obtained high agreement sequences that were morphologically identified six samples as A. bicolor bicolor and one sample as A. marmorata. Construction of the phylogeny tree indicated that intra-subspecies of A. bicolor bicolor had a close relationship and real apart from A. marmorata with a genetic distance range of 0.051-0.053. A. bicolor bicolor sequences of each river mixed and merged into one group. Molecular identification had shown taxonomy status of Anguilla spp. in several rivers that flow to Palabuhanratu Bay, Consequently, it could be determined for appropriate management.