Liriomyza trifolii (Burgess) and Liriomyza huidobrensis (Blanchard) are important vegetable pests in California. Populations of each species differ in their impact in central and southern regions. This difference may be explained by geographical or host plant differences in each of the regions. We used random amplified polymorphic DNA polymerase chain reactions to assess genetic differences between two laboratory populations of each species collected from central and southern California. Individual L. trifolii from the two regions could be discriminated by the presence/absence of PCR products. No such qualitative differences were apparent in PCR products amplified from L. huidobrensis individuals, but the origins of individuals could be differentiated using a bootstrap analysis of marker frequencies. Marker primers were used to compare field and laboratory individuals. No evidence was found for the existence of further populations or of hybrid populations in central and southern California. The distribution of populations of L. huidobrensis was explained completely by geographical differences. As a consequence of the absence of leafminer infestations on the same host plant varieties in both regions, factors governing L. trifolii population distribution differences were less apparent. The presence of the same host plant varieties at both sites suggests that the two L. trifolii populations differ in host plant preference.