Yongeichthys criniger belongs to Gobiidae, Gobioidei, and Perciformes in taxonomy. Its mitochondrial genome was first determined, which consists of 13 typical vertebrate protein-coding genes, 22 tRNA, 2 rRNA genes, and 1 control region. The mitogenome base's composition is 27.28% for A, 26.12% for T, 28.98% for C, and 17.62% for G. The phylogenic analysis involves 32 Gobiidae species in GenBank database. The results will provide more molecular information for the further studies on species identification and phylogenic evolution of Gobiidae.