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The complete mitochondrial genome of Pseudemys peninsularis in Korea was sequenced and characterized. The mitochondrial genome is constituted of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes) and a noncoding region. Phylogenetic analysis based on the 13 protein-coding gene sequences showed that P. peninsularis has closer relationship with Chrysemys picta than Trachemys scripta elegans. This is the first case for a complete mitochondrial genome from P. peninsularis, which will provide information for biogeographical studies and management plans for invasive species.