DNA sequence analysis of the mitochondrial cytochrome oxidase I (COI)-leucine tRNA (tRNA^Leu)-cytochrome oxidase II (COII) regions was performed to elucidate the phylogenetic relationships among 465 summer and winter-form psyllids from Saga and Yamaguchi prefectures in Japan. Multiple alignments of these sequences revealed 2 single-nucleotide polymorphisms (SNPs) at nucleotide positions 78 and 258 in the COI and tRNA^Leu regions, respectively. Based on the nucleotide changes at these loci, these 465 insects were grouped into 3 genotypes: 78A/258A, 78G/258G, and 78G/258A. All but 2 of the 225 insects in Saga belonged to the genotype 78A/258A, and the 2 exceptions belonged to the genotype 78G/258G. Conversely, all the insects (105) collected from Shimonoseki city in western Yamaguchi prefecture belonged to the genotype 78G/258G, while eighty percent of the 135 samples from eastern Yamaguchi prefecture belonged to the genotype 78G/258G. Among the other 27 insect samples, 24 were 78G/258A and 3 were 78A/258A. Using POPTREE2, the psyllids were divided into 5 populations associated with the geographical distribution. The results suggest that the genetic population structure of these psyllids varied widely between Saga and Yamaguchi prefectures.