Epigenetic gene regulation is one of the most exciting topics in biology today. The Y chromosome of Drosophila offers a unique opportunity to connect epigenetic regulation to specific adaptive traits. This 40 Mb chromosome is gene-poor and degenerate, with very little polymorphism in unique sequences owing to lack of recombination, exclusive transmission through males, and reduced effective population size. The Y chromosome has long been thought to have little role in phenotypic variation beyond a few Y-linked male fertility factors. We have described a new phenomenon termed Y-linked regulatory variation that affects the level of expression of hundreds of genes across the genome. We have shown that (1) these effects are largely, if not exclusively, epigenetic effects of microsatellites and other repeated sequences on the Y; and (2) Y chromosomes from natural populations are polymorphic for their effects on autosomal and X chromosomal gene expression. We have also shown that Y chromosomes from closely related species show Y-linked regulatory divergence and that these effects are associated with differences in male reproductive fitness. This project provides the first opportunities to associate specific repetitive DNA sequences on the Y chromosome to specific adaptive traits, to identify the networks of genes that are responsive to Y-linked regulatory variation, and to study Y-linked regulatory divergence and its association with male fitness in regard to implications for speciation.