We surveyed a 1,033-bp fragment of the cytochrome oxidase subunit I (COI) sequence to look for a useful diagnostic marker for discrimination between the Japanese cryptic species Chrysoperla nipponensis (Okamoto) (Neuroptera: Chrysopidae) (types A and B) and the commercially introduced Chrysoperla carnea s. str. from Germany. Phylogenetic analysis showed four distinct haplotype groups: one group corresponded to C. nipponensis type B and one group to C. carnea s. str., and the remaining two distinct groups, A1 and A2, corresponded to the same song phenotype, C. nipponensis type A. A2 was linked with the group of C. carnea s. str. and A1 was linked with the group of C. nipponensis type B. Cross-testing between A1 and A2 revealed their reproductive compatibility. Mitochondrial polyphyly within C. nipponensis type A may, therefore, originate from introgression or incomplete lineage sorting. Within the mitochondrial COI region presented here, there were 17 variable nucleotide sites useful for discriminating the four haplotype groups from each other.