A multiplex polymerase chain reaction (PCR) method was applied to differentiate thelytokous and arrhenotokous strains of Neochrysocharis formosa (Westwood). Alignment of strain first internal transcribed spacer regions revealed high nucleotide variability and the strain-specific primer sequence used. Strains were easily differentiated after gel electrophoresis of multiplex PCR products because arrhenotokous specimens produced a 500-bp fragment as well as the 800-bp fragment common to both strains. This method successfully distinguished N. formosa strains regardless of collection site across Japan; thus, it is probably suitable for similar applications in Turkey, Italy, and elsewhere.