In a natural population, we document changes in the frequencies of alMes influencing body size and size-correlated alternative male reproductive tactics, and we examine the possible role of sexual selection in producing these changes. Male swordtails (Xiphophorus nigrensis, Rio Choy) exhibit three body size class- es (small, intermediate, and large) that primarily derive from allelic variation (s,/, L) at the Y-linked pituitary (P) locus. Some XX individuals are male. They are small and can be fathered either by XX or XY males. We compared the frequencies of Y-linked P alleles across two generations in a natural population. There was a significant decrease in the Y-s genotype relative to Y-I and Y-L genotypes. Laboratory experiments suggest that the disadvantage of Y-s resulted, at least in part, from female preference for larger courting males relative to small chasing males. All larger courting males are of the Y-I or Y-L genotypes. Although the frequency of Y-linked P alleles changed across generations, there was no change in the distribution of male body size classes. The stability of the phenotypic distribution across generations, despite changes in P allele frequencies, was maintained by the production of small XX sons by Y-I and Y-L males.