Molecular technologies now allow researchers to isolate quantitative trait loci (QTLs) and measure patterns of gene sequence variation within chromosomal regions containing important polymorphisms. I develop a simulation model to investigate gene sequence evolution within genomic regions that harbor QTLs. The QTLs influence a trait experiencing geographical variation in selection, which is common in nature and produces obvious differentiation at the phenotypic level. Counter to expectations, the simulations suggest that selection can substantially affect quantitative genetic variation without altering the amount and pattern of molecular variation at sites closely linked to the QTLs. Even with large samples of gene sequences, the likelihood of rejecting neutrality is often low. The exception is situations where strong selection is combined with low migration among demes, conditions that may be common in many plant species. The results have implications for gene sequence surveys and, perhaps more generally, for interpreting the apparently weak connection between levels of molecular and quantitative trait variation within species.