As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci-hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)-to small nuclear genomic regions (each ,70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species.KEYWORDS speciation; hybrid incompatibilities; postzygotic reproductive isolation; Mimulus; monkeyflower S PECIATION occurs when diverging populations accumulate genetic differences that cause reproductive isolation. Many forms of prezygotic reproductive isolation likely evolve as byproducts of adaptation to different ecological conditions (e.g., habitat or behavioral differences), but the evolutionary dynamics of intrinsic postzygotic isolation are less clear. This is because the production of dead or sterile hybrids cannot be favored by natural selection. Dobzhansky (1937) and Muller (1942) proposed a solution to this long-standing mystery (Darwin 1859), explaining that a new mutation might function perfectly well with alleles present in its native species, and only cause sterility or inviability when found in a hybrid genetic background. The so-called Dobzhansky-Muller model shows that natural selection need not oppose the evolution of hybrid dysfunction, but it makes no predictions about the nature of the genetic changes or the evolutionary forces that give rise to hybrid incompatibilities.The recent identification of several hybrid incompatibility genes in diverse taxa has begun to reveal some insights into the evolution of hybrid dysfunction (reviewed in Presgraves 2010; Maheshwari and Barbash 2011;Sweigart and Willis 2012). In Arabidopsis and rice, genetic incompatibilities have been mapped to duplicate genes that carry loss-of-function alleles in alternate copies (Bikard et al. 2009;Mizuta et al. 2010;Yamagata et al. 2010), suggesting that divergence among paralogs via mutation and genetic drift might cause postzygotic reproductive isolation (Lynch and Force 2000). There are also hints that natural selection can contribute to the spread of incompatible alleles within populations and species. For example, ...