Abstract: Oxynoe nanhaiensis sp. nov., a small green sea slug discovered in the coastal waters of the South China Sea, was investigated in this study. By analyzing the mitochondrial genomic characteristics and constructing phylogenetic trees, this research aims to determine its taxonomic status and contribute to the documentation of sacoglossan species diversity in China. The complete mitochondrial genome, obtained using next-generation sequencing (NGS) technology, is 16189 bp in length and comprises 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 non-coding regions. The nucleotide composition exhibited high A+T and low G+C content bias. Among the protein-coding genes, four types of start codons (AUG, GUG, UUG, AUA) and three types of stop codons (TAG, TAA, and T) were identified, with an overall AT bias and weak negative AT skew. In the predicted secondary structures of tRNAs, eight could form the typical cloverleaf structure, while the remaining 14 lacked key elements such as the DHU arm or TΨC arm. A maximum likelihood (ML) phylogenetic tree was constructed using mitochondrial genomes of species with high sequence similarity and comparable genome sizes placed O. nanhaiensis in a clade with Ascobulla fragilis, though limited availability of mitochondrial genomic data from closely related species. In a cox1-based phylogeny using Phyllidiella nanhaiensis (a non-sacoglossan species) and Elysia tomentosa (a shell-less sacoglossan species) as outgroups, O. nanhaiensis clustered with other members of the genus Oxynoe. Genetic distances of the cox1 gene between O. nanhaiensis and three species—O. kylie, O. jordani, and O. viridis—were 5.00, 3.93, and 5.15, respectively. Combined with morphological characteristics and molecular identification, the results confirm the establishment of Oxynoe nanhaiensis, sp. nov. as a new species. PCR amplification of chloroplast gene fragments within the species showed over 94% similarity to multiple algal species, suggesting the presence of kleptoplasty, a feature consistent with some sacoglossan species. This study presents the first mitochondrial genome characterization of a new species in the genus Oxynoe and clarifies the phylogenetic position of Oxynoe nanhaiensis sp. nov., providing important data for research on the diversity, phylogeny, and evolution of sacoglossan species.