Samples were obtained through field sampling from the South China Sea, but the species could not be identified by their appearance. Therefore, the study used complete mitochondrial genome sequencing to identify, analyzed the phylogenetic relationship, and named it Phyllidiella pustulosa nanhai. The mitochondrial genome of P. pustulosa nanhai was 14677 bp in length, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The base composition of mitogenome is 30.37% for A, 37.30% for T, 15% for C, and 17.33% for G, with a preference for AT, and the content of AT was 67.67%. Among the 13 protein-conding genes, there were 11 start codon conformed to the codon form of ATN, except for ND5 and ND6 which uses TTG. There are 9 protein-conding genes with a termination codon of TAA and TAG, and the other 4 protein-conding genes were terminated as T. The phylogenetic tree showed that P. pustulosa nanhai was closely related to P. pustulos, followed by Phyllidia ocellata. The mitogenome of P. pustulosa nanhai will provide a reference for the mitogenome of sea slug and will be valuable for future research related to the diversity and phylogeny of sea slug.