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Background: There is an increasing pressure on tropical species of the freshwater eel genus Anguilla for use in aquaculture, so species identification methods are needed to monitor these activities and to facilitate conservation efforts. A method was developed to genetically distinguish two subspecies of the Indonesian short-finned eel, Anguilla bicolor, based on an allelic discrimination technique. Results: A single DNA nucleotide substitution in the mitochondrial DNA 16S rRNA gene was employed to identify the two subspecies where Anguilla bicolor bicolor and Anguilla bicolor pacifica possessed adenine and guanine, respectively. This substitution was highly conserved at 100% in A. bicolor bicolor (108/108) and 99.9% in A. bicolor pacifica (181/182), and the misidentification rate was estimated to be 0.34%. Subsequently, fluorescent-labeled oligo probes and PCR primers were designed and succeeded to clearly distinguish the two subspecies. Further, the other ten anguillid species that may be sympatrically distributed with A. bicolor showed negative results. Conclusions: The method developed in this study is useful to accurately identify the two subspecies of A. bicolor and can contribute to ecological studies, stock management, and conservation.

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Species-specific restriction fragment length polymorphism in the intron of the androgen receptor gene (ar5) was found in glass to silver-stage individuals of Anguilla japonica (n = 51) and A. marmorata (n = 21). The sequence analysis of 16S rDNA from 328 anguillid leptocephali collected in the North Equatorial Current of the western North Pacific Ocean revealed the specimens to be A. japonica (n = 194), A. marmorata (n = 128), A. bicolor pacifica (n = 5) and A. luzonensis (n = 1). All leptocephali of A. japonica and A. marmorata were monomorphic and did not share an allele at the ar5 locus, indicating that the two species are reproductively isolated.

To investigate the species composition and genetic characteristics of Far Eastern daces, genus Tribolodon, in the Tama River, Japan, partial DNA sequences of the mitochondrial DNA control region were compared among specimens from the whole river system. Specimens of Tribolodon hakonensis (n = 257) and Tribolodon brandtii maruta (n = 193) were examined in this study. Inconsistencies in species identification according to genetic and species-specific morphological traits, i.e., breeding color and cephalic lateral line system, were found between some sympatrically distributed specimens (17/450; 3.8%), indicating possible hybridization between T. hakonensis and T. brandtii maruta. The two species were sympatrically distributed in the lower reaches, whereas T. hakonensis solely appeared in the upper reaches and headwaters. In T. hakonensis, we found obvious genetic divergence between the lower and upper reaches, suggesting reproductive isolation related to alternative migration patterns of anadromous and river-resident forms, respectively. Further, it is suggested that native and introduced T. hakonensis populations coexist in the lower reaches and headwaters, whereas the former solely inhabit, or are dominant, in the upper reaches.