The apple maggot fly, Rhagoletis pomonella, is a significant pest of cultivated apples. This fly has undergone a host shift from its native hawthorn fruit (Crataegus spp.) within 200 years of the introduction of apples to form two partially reproductively isolated host races. The very recent host shift suggests rapid adaptation and selection for certain traits pertaining to the infestation of apples, such as an earlier eclosion. Previous studies have suggested that chromosomes 1-3 harbor genetic adaptations and differentiation among the host races, with chromosomes 4-6 playing a limited role. However, difficulties in quantitative trait loci mapping and the limited extent of the genome analyzed may point to the presence of other genomic regions displaying genetic differentiation. In this study we used 38 microsatellite markers distributed among chromosomes 1-5 to analyze signatures of selection based on latitudinal clines within and between the two host races. Samples were collected along a North-South transect from northern Michigan to northern Mexico from 6 populations, 3 of which contained sympatric collections of both apple and hawthorn flies. Preliminary evidence suggested that, as found previously with allozymes, microsatellite loci on chromosomes 1-3 exhibited significant allele frequency clines. However, results also indicated evidence of allele frequency clines with loci on chromosomes 4 and 5, implying that a larger proportion of the genome than previously thought may be under selection. Genome wide genetic differentiation within and among host races will be discussed, including the influence of latitudinal environmental clines in maintaining these genetic differences.