Genomic DNA from two isolated gregarious locust populations in Africa had been amplified by using short decamer primers of random sequences. To identify markers that may distinguish between two major locust populations, northern Schistocerca gregaria gregaria, and southern Schistocerca gregaria flaviventris, 20 operon kit (A) primers from both populations were investigated with genomic DNA. Four primers generated low molecular weight polymorphic patterns. The primer (A2) showed a particular DNA amplified band (∼600 bp) from the southern S. g. flaviventris that was not expressed in the northern S. g. gregaria. For further examination, southern blot hybridisation indicated that this sequence is extremely repeated in the genome of the S. g. flaviventris population but not to the northern population. Therefore, this sequence may be highly specific to the southern locusts. Also, the southern population may constitute an evolutionary dichotomy that occurred on the African continent and can separate the populations of the two locusts into two distinct species.