Project description:Three-spot angelfish (Apolemichthys trimaculatus) is one of the most widespread angelfish that belongs to Pomacanthidae. However, there are few reports of the systemically classification and evolutionary analysis for A. trimaculatus so far. In this study, the complete mitochondrial genome of the A. trimaculatus is described. The full length of the mitogenome is 16,548 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region. The overall base composition is 28.4% for A, 25.6% for T, 29.5% for C, and 16.5% for G, with a slight AT bias (54.0%). The mitogenome of A. trimaculatus provided essential and valuable DNA molecular information for further phylogeny and management of angelfish species.