Carybdea brevipedalia Kishinouye, 1891 is a poisonous jellyfish that usually occurs only in Japanese coastal regions. However, it was recently found on the Korean coast, thus expanding its known geographical range. In this study, we analyzed the population genetics and demographic histories of 113 C. brevipedalia specimens from the southern and eastern coastal regions of Korea by sequencing mitochondrial DNA cytochrome c oxidase subunit I (COI). We identified 42 C. brevipedalia COI haplotypes with high genetic diversity and a significant genetic structure. Populations were highly differentiated based on geographic location and distinctly divided into A and B clades. The results of Mantel tests indicated that geographic distance influenced the genetic distance between the two clades. Moreover, demographic analyses (neutrality tests) and the star-like profile of the Templeton, Crandall, and Sing (TCS) haplotype network indicated that C. brevipedalia had recently expanded into the southern and eastern coastal regions of Korea. These findings suggest that C. brevipedalia populations along the Korean coast have significant genetic differentiation that could be influenced by geographic isolation and subsequentadaptation to regional ecological conditions.