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We here report the complete mitochondrial genome of Chrysichthys nigrodigitatus, which is 16,514 bp in length. Mitogenome of C. nigrodigitatus showed the conserved 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions including the light-strand replication origin (OL) and a putative control region (CR). All tRNA genes were predicted to fold into the typical cloverleaf secondary structures with the typical base-pairing except for tRNA-Ser(AGC). Phylogenetic analysis with currently known complete mitogenome sequences in Siluriformes showed that C. nigrodigitatus is most closely related to Auchenoglanis occidentalis forming a family Claroteidae cluster.