Experiments were conducted to assess the efficiency of RAPD and PCR-RFLP marker systems as molecular tools for taxonomy and classification of insects. Three species of adult ants, Camponotus maculatus, Monomorium pharoensis and Cataglyphis bicolor, were used in this study. Total genomic DNA was extracted and used for PCR amplification of the ITS region. The purified PCR products were subjected to single digestion with EcoRI, MspI, TaqI and SacI enzymes and visualized on 2% agarose gel. In addition, 40 arbitrary primers were used to generate RAPD-PCR profiles. Data obtained from RFLP, RAPD and RFLP+RAPD were statistically and phylogenetically analyzed to determine the level of polymorphism in each case. Intraspecific, interspecific variation levels and phylogenetic relationships were investigated. Results were discussed, comparatively, and the final conclusion was: on the bases of ease, cost, technical labor, speed and amount of DNA needed, the RAPD marker system is preferentially used in taxonomic and classification studies. On the bases of degree of polymorphism, precision of genetic distance estimates and the statistical power of the test, no differences were observed between RAPD and PCR-RFLP tests.