Rhagoletis pomonella group species (Diptera: Tephritidae) are of interest for studying evolutionary processes as well as for their status as pests of fruit crops. Here we report the use of amplified fragment length polymorphism (AFLP) data to examine three pomonella group species, R. pomonella (Walsh), R. zephyria Snow, and R. mendax Curran, with respect to population genetic structure, species relationships and species identification. Our goals were to determine if we could use AFLPs to recover R. pomonella, R. mendax and R. zephyria as separate species, to identify sister species, and to determine the polarity of the evolution of these three species. AFLP profiles were obtained using two selective primer pair combinations from fifteen R. pomonella populations, fifteen R. zephyria populations, and eight R. mendax populations. Data were analyzed to obtain estimates of genetic diversity and genetic differentiation within and among the three species. Phylogenetic analysis indicates that each of the three species forms a coherent cluster, with R. mendax and R. pomonella as sibling species. However, these results do not have bootstrap support. AFLPs may potentially be useful to distinguish between field-caught R. zephyria and R. pomonella in areas where these two species co-occur (e.g., Washington State). There appear to be combinations of AFLP bands (genotypes) that uniquely identify individuals to the species level. However, our results are complicated by apparent low levels of introgression of R. zephyria alleles into R. pomonella populations. In addition, we discuss technical challenges associated with the implementation of AFLP analysis for species identification.