The genus
Rhinogobius
was widely distributed in East Asia. In the present study, the complete mitochondrial genome of
Rhinogobius
sp., possible a new species of freshwater goby from Anhui province of China, was sequenced for the first time. Sequence analysis showed that it is 16,511 bp in length with A + T content of 52.3%, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (CR). Phylogenetic analyses placed
Rhinogobius
sp. in a well-supported monophyletic cluster with other
Rhinogobius
fish and the phylogenetic position of
Rhinogobius
sp. was closer to
Rhinogobius cliffordpopei
.