We report the complete mitochondrial genome of
Rhinogobius lentiginis
, which was found to be a circular molecule of 16,633 bp in length and included 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region. The overall base composition was 28.44% A, 26.21% T, 16.33% G, and 29.02% C. Phylogenetic analyses using maximum-likelihood and Bayesian inference methods revealed a close genome relationship among
R. lentiginis
,
R. niger
,
R. shennongensis
and
R. maculagenys
. The complete mitogenome of
R. lentiginis
will provide a valuable resource for species classification and conservation.