Presented is a phylogenetic reconstruction of mudskippers using sequences of the mitochondrial COI and cytb genes. The phylogeny combines the sequences of 12 species from GenBank with those of three species (Boleophthalmus dussumieri, Periophthalmus waltoni and Scartelaos tenuis) collected from the coastal area of the Persian Gulf and Oman (Makran) Sea and sequenced for the first time. Based on the Maximum likelihood and Bayesian methods, Periophthalmus forms a separate clade that is the sister lineage to a group formed by all remaining genera. The subfamilies Oxudercinae and Amblyopinae established on the basis of morphological characters have been shown to be paraphyletic and their use as taxonomic units is no longer recommended. The evolution of Periophthalmus waltoni, Periophthalmus barbarous and Boleophthalmus dussumieri is discussed based on molecular phylogenetic reconstruction.

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