Reciprocal molecular markers were developed to distinguish the closely related parasitoid genera Encyrtus Latreille, Metaphycus Mercet and Paraceraptrocerus Girault (Hymenoptera : Encyrtidae). These parasitoids are widely used in the biological control of soft scales and based upon morphology, it is extremely difficult to distinguish them. DNA extraction and RAPD-PCR were used to assess the amount of genetic variation within and among species at this locus. From parsimony analysis, populations of Encyrtus inflelix (Embleton), Metaphycus anneckei Guerrieri & Noyes and Paraceraptrocerus africanus Giralut were separated. Specific DNA markers of E. inflelix, P. africanus and M. anneckei at M.W. of (475.07, 429.60, 311.37bp) and (473.33bp), (700.0, 400.0 and 270.59bp) and, (918.79, 814.45, 771.44bp) for (AC07), (AE02), (B10) and (B07) primers, respectively were used. Based upon the sequence variation among species, the present study appeared a simple molecular assay to rapidly and unambiguously distinguish E. inflelix, P. africanus and M. anneckei species.