Sexually deceptive orchids from the genus Ophrys attract their pollinators primarily through the chemical mimicry of female hymenopteran sex pheromones, thereby deceiving males into attempted matings with the orchid labellum. Floral odor traits are crucial for the reproductive success of these pollinator-limited orchids, as well as for maintaining reproductive isolation through the attraction of specific pollinators. We tested for the signature of pollinator-mediated selection on floral odor by comparing intra and interspecific differentiation in odor compounds with that found at microsatellite markers among natural populations. Three regions from southern Italy were sampled. We found strong floral odor differentiation among allopatric populations within species, among allopatric species and among sympatric species. Population differences in odor were also reflected in significant variation in the attractivity of floral extracts to the pollinator, Colletes cunicularius. Odor compounds that are electrophysiologically active in C. cunicularius males, especially alkenes, were more strongly differentiated among conspecific populations than non-active compounds in the floral odor. In marked contrast to these odor patterns, there was limited population or species level differentiation in microsatellites (F_ST range 0.005 to 0.127, mean F_ST 0.075). We propose that the strong odor differentiation and lack of genetic differentiation among sympatric taxa indicates selection imposed by the distinct odor preferences of different pollinating species. Within species, low F_ST values are suggestive of large effective population sizes and indicate that divergent selection rather than genetic drift accounts for the strong population differentiation in odor. The higher differentiation in active versus non-active odor compounds suggests that divergent selection among orchid populations may be driven by local pollinator preferences for those particular compounds critical for pollinator attraction.