| Summary: | We newly sequenced complete mitochondrial genomes (mitogenome) of two gudgeon species <i>Saurogobio dabryi</i> and <i>S. punctatus</i>, and we downloaded 49 gudgeon mitogenomes from GenBank to investigate the phylogeny of the Pseudogobionini group and analyze selection pressure of the genes. With genera <i>Gobio</i>, <i>Acanthogobio</i>, and <i>Romanogobio</i> as outgroups, the phylogeny of the Pseudogobionini group was revealed as ((<i>Xenophysogobio</i> + <i>Gobiobotia</i>) + (<i>Saurogobio</i> + (<i>Abbottina</i> + (<i>Pseudogobio</i> + <i>Biwia</i> complex)))) based on the concatenated nucleotide sequences of 13 protein-coding genes (PCGs). Based on the molecular phylogeny and morphological or osteological characters, we proposed a classification system of the Pseudogobionini group. Moreover, five pairs of sister taxa were selected for gene selection pressure analyses to explore the link of mitochondrial gene evolution to group differentiation and adaptations. We detected significantly different dN/dS values in 11 out of 13 (excluding <i>ND3</i> and <i>ND4L</i>) PCGs in five pairs of clades, significantly different mean dN/dS, dN, and/or dS values in 8 out of 13 PCGs (excluding <i>ND2</i>, <i>ATP8</i>, <i>ND3</i>, <i>ND4L</i>, and <i>ND6</i>) in three pairs of sub-clades and seven positively selected sites in another three pairs of sub-clades. These results indicated that mitochondrial gene evolution might have contributed to group differentiation and adaptations especially for river or lake environments.
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