Psyllids are a menacing pests of pears (Pyrus spp.) grown in temperate and subtropical regions of the world, including Taiwan and China. Pear psyllids belong to the large genus Cacopsylla (Psyllidae: Psyllinae). Among the 28 psyllid species that infest pear trees, Cacopsylla chinensis (Yang and Li, 1981) is considered the most harmful. Two psyllid outbreaks involving exotic species affected Japanese pear (Pyrus pyiifolia variety culta) orchards in the Saga Prefecture in July and November 2011. The psyllids were morphologically identical to the summer and winter forms of C. chinensis. In this study, we performed DNA sequence analysis of the mitochondrial cytochrome oxidase I-leucine tRNA-cytochrome oxidase II (COI-tRNA^Leu-COII) and 16S rDNA regions to elucidate the phylogenetic relationships among 82 summer-form psyllids, five winter-form psyllids from several orchards in Japan, and those reported from Taiwan and China. The sequences of the COI-tRNA^Leu-COII and 16S rDNA regions were identical among all 87 psyllids from Japan, regardless of summer/winter forms or orchards in Saga, Japan. Comparison of nucleotide sequences and phylogenetic analysis differentiated Japanese psyllids from the Taiwanese and Chinese C. chinensis isolates, with ≈8 and 7% nucleotide difference in the COII-RNA^Leu-COII and 16S rDNA regions, respectively. The results suggest that C. chinensis possess a high level of genetic variability and that the psyllids responsible for the outbreak in Saga, Japan belong to a distinct lineage of C. chinensis.