Parasitoid insects that use different hosts can have a subdivided population structure that corresponds to host use. A subdivided population structure may favor local adaptation of subpopulations to small-scale environmental differences and may promote their genetic divergence. In this paper, heritable Random Amplified Polymorphic DNA (RAPD) markers visualized by single strand conformational polymorphisms (SSCP) analysis were used to examine the population structure of the parasitoid wasp Diaeretiella rapae (Hymenoptera: Braconidae) in an environment where two aphid hosts are available for oviposition. We found 11 codominant and 34 dominant RAPD polymorphisms that conformed to Mendelian segregation patterns. A nested analysis of variance indicated extensive genetic differentiation among six populations of D. rapae that were sampled for two years. Effective migration rates (Nm) between populations ranged from 1.2 – 1.6, indicating a relatively low dispersal rate. Genetic distances were also calculated between populations and the resulting trees indicated that populations less than 1.0 km from each other were genetically differentiated. Our results indicate that D. rapae populations are genetically subdivided on a small spatial scale that corresponds to host use patterns.