The JpL species is one of the 36 species belonging to the Bemisia tabaci complex and is distributed in two countries, Korea and Japan. To clarify genetic relationships among different populations of the JpL species in Korea, 83 cytochrome oxidase subunit I (COI) sequences generated from 83 individuals collected from eight Korean provinces were analyzed together with the published 16 Korean COI sequences. A total of eight haplotypes were detected from the 99 COI sequences, and 82 COI sequences shared one haplotype, hap-2. The remaining 17 COI sequences were assigned to seven haplotypes, hap-1, 3, 4, 5, 6, 7, and 8. The median-joining networks of the eight haplotypes revealed that the Korean JpL species has undergone genetic variations separately according to two groups, Korean Peninsula and Jeju Island. In addition, the phylogenetic trees constructed based on the 99 COI sequences and published seven Japanese COI sequenceswere divided into two clades: clade (A) consisted of 97 COI sequences from the Korean Peninsula group, and clade (B) consisted of 19 COI sequences from the Jeju Island and Japan groups. Our study suggests that the Korean populations of the JpL species might have spread and be undergoing genetic variations separately according to the two groups, Korean Peninsula and Jeju Island.