ABSTRACT. – Indonesian waters, have been proposed by biologists to be the origin of freshwater eel anguillid. The objective of this study was to investigate molecular phylogenetic relationships and genetic diversity of the seven Indonesian eel taxa based on the cyt b gene. Each eel species was identified by comparison with published sequences, namely Anguilla celebesensis, A. interioris, A. borneensis, A. marmorata, A. bicolor bicolor, A. b. pacifica and A. nebulosa nebulosa. A total of 129 different haplotypes were identified from this study, most of them for the first time, showing haplotype and nucleotide diversities of 0.98 and 4.57 %, respectively. A. bicolor was clearly found to be composed of two subspecies, A. b. bicolor and A. b. pacifica. The first subspecies was split into two major clades supported by a high bootstrap value, with each clade characterized by two diagnostic nucleotides. A. marmorata was also split into two clades, supported by a high bootstrap value. This first study of phylogenetic relationships and genetic diversity from all Anguilla taxa inhabiting Indonesian waters, based on 1115 specimens, is necessary for a local management and conservation of this valuable resource in terms of both biodiversity and economic development.