Aedes albopictus is one species of mosquito transmitting flavivirus causing Dengue, Zika, and West Nile fever. Although it is an important disease vector, the genetic study of Ae. alpopictus populations has not been undertaken yet in South Korea. Here, we investigated the genetic variation of 99 Ae. albopictus individuals collected from 29 sites in nine provinces in 2016, through mitochondrial COI gene analysis. Haplotype analyses revealed seven haplogroups in South Korea. The main haplogroup, comprising 76 individuals (77.8%), was genetically identical to the one from Nagasaki. Two groups from Jeju Island (11) and the southern coast of South Korea (nine) were closely related to different Ae. albopictus strains from Kumamoto and Guangdong/Fujian, respectively. However, the others (four) were distinct from these two countries. No geographic divisions of populations were found in the study regions. The results suggest the possibility that the currently prevalent Ae. albopictus in South Korea, represents a part of the descendants that originated from nearby countries. However, more comprehensive investigations are needed to explain its movement routes.