We have used the polymerase chain reaction (PCR) and the random amplified polymorphic DNA (RAPD) method to identify DNA polymorphisms that can be used as genetic markers to characterize populations of the Mediterranean fruit fly, Ceratitis capitata. In this study, RAPD markers have been used to resolve genetic variability between populations of this major agricultural pest species. The populations analyzed represent either laboratory stocks or wild collections originating from different geographic localities. Using the same set of individual flies from each of several populations, we show that the use of different primers in the RAPD method permits detection of different levels of population differentiation. We show results from RAPD primers (e.g., primer 14) that identify regions of the genome (through PCR amplification) that are essentially monomorphic in all flies originating from a particular geographic locality. We also show RAPD primers (e.g., primer 67) that identify what appear to be highly variable regions of the genome. We have used primers of this type to produce genetic markers that can distinguish even between laboratory versus wild populations as well as subpopulations of flies from more broadly defined geographic localities, such as within the Hawaiian islands. These results show that the RAPD method is a broadly applicable, high resolution method for documenting genetic variability within and between populations of insect pest species.