The honey bee, Apis mellifera ligustica (Hymenoptera: Apidae), strain with a high hygienic behavior (HHB) has been bred for several years in Korea, and a diagnosis system to distinguish it from low hygienic behavior (LHB) strain has been necessitated. Thus, complete mitogenome of the two strains were sequenced through Next-Generation Sequencing technique to detect SNPs. Comparison of the mitogenome sequences from the two strains of A. m. ligustica have detected 23 SNPs in 11 PCGs and these were further confirmed the presence of SNPs using each 10 individuals selected randomly from each strain, indicating that these SNP markers might be useful to diagnose the honeybee strains with the HHB. Therefore, mitogenome sequences are promising genome source to detect SNP markers, particularly for inbred female iso-lines.