(Trichiuridae) has historically been challenging because of the morphological similarities between the species. As a result, Linnaeus, 1758 was recognized as a monotypic cosmopolitan species of Li, 1992, based on morphological differences in the skull patterns and dorsal fin coloration, i.e.supraoccipital bone with a hard knob and yellow dorsal fin respectively. Subsequently, Yamada et al. described with a yellow dorsal fin from the Ryukyu Islands and East China Sea coast of Kyushu, Japan. This species is very similar to , but shows some variation in the size of a pair of knobs on the supraoccipital crest. Accordingly, the yellow dorsal fin species of sp. 2 by Nakabo. There remains no molecular evidence that elucidates the genetic differences between . sp. 2 (sensu Nakabo, 2002). Thus, the phylogenetic relationship and taxonomic status of these two species remain unresolved. individuals collected from the coast of western Hainan Island (Baimajing, Yinggehai and Sanya), South China Sea, China The 16S rRNA genes were amplified using PCR techniques. Homologous sequences from .sp. 2 and closely-related species from previous studies were also included in the comparative analysis. Genetic information indexes, including base composition, sequence variation, and Kimura-2 parameter net genetic distance were examined. Phylogenetic analysis using neighbor-joining (NJ) and maximum-likelihood (ML) methods were conducted using There was evidence of insertion or deletion of base pairs in the 435 bp sequence alignment, with 63 variable sites, 48 parsimony informative sites, and 15 singleton sites. The net genetic distances between . sp. 2 (from Japan, eastern , and Indian Ocean) ranged from 0.000 to 0.006. These values were much lower than those found for interspecific 16S rRNA comparisons in some species of (0.037–0.061), and for intraspecies comparisons between populations of . sp. 2 did not form reciprocal monophyletic clades in the phylogenetic trees (NJ, ML), and the close relationship of the haplotypes of these two species was supported by high confidence levels (NJ 100%, ML 99%). These results indicated that the genetic distance between . sp. 2 (sensu Nakabo, 2002) from Japan should be classified as is widely distributed from the Indian Ocean to the western Pacific, and not merely limited to the South China Sea, Taiwan Strait, and Taiwan coastal waters. Based on coalescent estimates of divergence times among species, the origin and evolution of