The morphological characters of Cirrochroa aoris (Large Yeoman) and C. tyche (Common Yeoman) are very similar making identification confusing and difficult. The genomic DNA of the two species was subjected to RAPD-PCR analysis with six decamer oligonucleotides, i.e. MA5, MA6, MA8, OPB12, OPT4 and OPT5. All of them produced discrete bands of various lengths revealing genetic variations as well as similarities between the two species. A total of 50 RAPD bands were generated with 45 polymorphic bands. The percentage polymorphism was 90.58% and all the similarity coefficients between the species were less than 0.2. Results showed a high genetic variation between the two cryptic species. Some species specific bands were obtained with these primers which can be considered as diagnostic bands. All the primers also produced species specific bands.