Members of the genus Awaous are found in fresh, brackish, and marine waters from Africa to the Americas, showing a circumtropical distribution, mostly found in the Indo-West Pacific region. There is some controversy surrounding the taxonomy and phylogenetic composition of species of the genus Awaous. Here, we carried out a mitochondrial phylogenomic analysis on the genus Awaous including newly sequenced of Awaous jayakari and published mitogenomes towards elucidating the phylogenetic relationship of the genus. The result of the Bayesian reconstructed phylogenetic tree almost confirmed Watson’s traditional classification with three main groups/subgenera. Within Awaous, 10 clades, mainly corresponding to separate nominal species, are resolved. Based on the first mitochondrial COI gene sequences of Omani population and also the detailed morphology of specimens collected from Oman and southeast Iran, their comparison with the type specimens, the Omani and Iranian populations of snout goby are taxonomically assigned to Awaous jayakari. The phylogenetic analysis failed to recover A. banana, A. ocellaris, and A. grammepomus sequences as monophyletic clusters. Awaous jayakari is sister to Awaous sp._Bangladesh (PP = 0.33), and these two species form a clade that is set apart with low statistical support value (PP = 0.24) Awaous sp._Kaladan basin, NE India from. Awaous jayakari showed the lowest mean K2P distance values with Awaous sp. Bangladesh (0.76), A. aeneofuscus (0.80), and Awaous sp. Kaladan basin (0.82) and the highest K2P distance value with A. melanocephalus (0.257). Data on A. jayakari would offer particularly valuable information on the phylogeny, biogeography, and conservation of amphidromous Awaous species. A narrow distribution range, low population size, presence in dried areas (Wadis), unknown biology and ecology, introduction of exotic fish elements, dispersal limitation, and its unique genetic features make it one of the most important inland fish candidates in conservation and management programs in Oman.
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