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In this study, we firstly reported the complete mitochondrial genome of Copadichromis trimaculatus. The whole mitochondrial genome is 16,581 bp in length, including 2 ribosomal RNA genes, 22 transfer RNA genes and 13 protein-coding genes. Its GC content is 46.00%, similar to Copadichromis virginalis (45.74%). We also analyzed its phylogenic relationship with other 14 related species, which would facilitate our understanding of the phylogenic relationship of Cichlidae mitochondrial genome.