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We reported the complete mitochondrial genome yielded by next-generation sequencing of Brochis multiradiatus in this study. The total length of the mitochondrial genome is 16,916 bp, with the base composition of 32.49% A, 25.47% T, 27.12% C, and 14.91% G. It contains 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is the same as that found in the Corydoras. The complete mitochondrial genomes of B. multiradiatus and other 12 species from Siluriformes were used for phylogenetic analysis using neighbor-joining method. The topology demonstrated that all species belong to four genera and are divided into two groups (Siluridae and Callichthyidae), the B. multiradiatus was clustered with genus Corydoras. Brochis multiradiatus’ molecular classification is consistent with the external morphological feature results, so the information of the mitogenome could be used for future identification of Brochis.