Much of the diversity of flowering plants is associated with genomic duplication through polyploidy. Little is known, however, about the evolutionary mechanisms responsible for the diversification of novel polyploid lineages. We evaluated the possibility that divergence is driven by natural selection by estimating the strength of phenotypic selection acting on three floral traits in sympatric populations of diploid and autotetraploid Heuchera grossulariifolia over three years. Our results demonstrate consistent directional selection for increasing scape length and floral display in both diploid and tetraploid populations. In contrast, selection acting on flowering phenology varied across year and ploidy. Specifically, selection was found to favor late-flowering diploids in 2001 and 2002 but early-flowering tetraploids in 2003. We investigated the mechanistic basis of divergent selection for flowering phenology in 2003 by estimating the relationship between plant flowering phenology and the probability of intercytotype pollinator movement. The results demonstrated that less divergent tetraploids were significantly more likely to experience intercytotype flights than were more divergent tetraploids. This result is consistent with the pattern of phenotypic selection observed. Taken together, our results suggest that divergence of polyploids and their diploid progenitors may be driven by a process analogous to reinforcement whereby selection favors phenotypes that reduce the probability of intercytotype matings with reduced fertility.