In On the Origin of Species, Darwin proposed that natural selection had a fundamental role in speciation. But this view receded during the Modern Synthesis when allopatric (geographic) models of speciation were integrated with genetic studies of hybrid sterility and inviability. The sympatric hypothesis posits that ecological specialization after a host shift can result in speciation in the absence of complete geographic isolation. The apple maggot, Rhagoletis pomonella, is a model for sympatric speciation in progress. Hawthorn (Crataegus spp.) is the native host for R. pomonella in N. Americas. But in the mid-1800s, a new population formed on introduced, domesticated apple (Malus pumila). Recent studies have conferred 'host race' status on apple flies as a potentially incipient species, partially isolated from haw flies owing to host-related adaptation. However, the source of selection that differentiates apple and haw flies is unresolved. Here we document a gene-environment interaction (fitness trade-off) that is related to host phenology and that genetically differentiates the races.