The Liriomyza trifolii (Burgess, 1880), Liriomya congesta (Becker, 1903), Agromyza apfelbecki Strobl, 1902 and Chromatomyia horticola (Goureau, 1851) species have become important vegetable pests in the agricultural areas in Turkey. These species are not easily differentiated by their morphological characteristics. The aim of the present study was to obtain genetic markers to unambiguously distinguish these species and gain insight into genetic variation between the individuals of L. trifolii strains collected from various geographic locations in Turkey. Thus, four random primers were employed to generate RAPD markers. Different RAPD profiles were observed for the different species indicating that the RAPD-PCR analysis can be applied as a useful tool in quickly screening the strains to aid in discriminating these species that was routinely done via classical methods. Identification of biotypes of the species is crucial in order to designing control strategies to avoid the spread of the pests because of economic losses caused by the damages to vegetable crops. Our results show that RAPD is promisingly an effective, fast and economic way, hence proposed as a valuable alternative to traditional identification of the insect species and strains