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Mitochondrial genomes of Squalidus mantschuricus, S. chankaensis, and S. longifilis have been determined using Sanger sequencing (GenBank Accession No. MT767745–MT767747). The three mitochondrial genomes consist of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region with the length of 16,605, 16,611, and 16,607 bp. Phylogenetic analysis of the three species showed that S. mantschuricus is nested within a fully supported terminal clade with S. argentatus, and S. chankaensis is a sister group of S. mantschuricus, S. argentatus, and S. wolterstorffi. Squalidus longifilis is positioned in a clade with S. multimaculatus and S. gracilis.

Mitochondrial genomes of two individuals of Tachanovsky’s gudgeon Ladislavia taczanowskii have been determined on the basis of Sanger dideoxy sequencing. The gene compositions of two genomes contain 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region with the same length 16,614 bp. The phylogenetic tree reveals that the monotypic genus Ladislavia is a sister group of the subfamily Gobioninae within the family Gobionidae.

Abbottina binhi has been misidentified as Abbottina rivularis in China for a long time. In this study, we determined three mitochondrial genomes of A. rivularis and A. binhi such that these data should contribute to molecular identifications of the two species. The size of new mitochondrial genomes was 16,609 or 16,599 bp with A + T bias of 55.7–56.5% in the base compositions. Our reconstructed phylogeny showed that A. rivularis and A. binhi formed a sister taxon relationship, and they together were a monophyletic group.

Freshwater fishes of the subfamily Gobioninae (Cypriniformes: Cyprinidae) are composed of three major clades, the tribes Gobionini and Sarcocheilichthyini, and a Hemibarbus–Squalidus group. In this study, we determined ten complete fish mitogenomes from eight of all twelve genera in the tribe Gobionini. The ten mitogenomes displayed similar patterns in gene arrangements, codon use and gene overlaps with the length of 16,605–16,617 bp and base compositions slightly A + T bias of 56.1–58.0%. Our phylogeny of the tribe Gobionini revealed that the genera Gobio, Xenophysogobio, Gobiobotia, Saurogobio and Pseudogobio were monophyletic, and other genera Abbottina, Biwia, Microphysogobio and Platysmacheilus were paraphyletic or polyphyletic. The findings indicate that the genera classifications of Gobionini are needed to be further confirmed.