As individuals and populations diverge ecologically, they become exposed to new parasites and pathogens with potentially harmful fitness consequences. Populations are therefore expected to evolve resistance, possibly at a cost of less resistance to parasites rarely encountered parasites. This trade-off in resistance should generate local adaptation to parasites in different habitats. In chapter one, I show how local adaptation can potentially evolve in response to variation in parasite exposure among eighteen ecologically variable populations of threespine stickleback (Gasterosteus aculeatus). Within populations infection appeared to reflect morphology/diet based exposure differences among individuals. Among populations, however, these patterns were absent or reversed, consistent with the evolution of local adaptation. In chapters two and three I set out to test whether variation major histocompatibility (MHC) genes can underly such local adaptation in stickleback. MHC genes are important components of vertebrate immunity; however, there is little direct empirical support for spatially divergent selection driving local adaptation on MHC loci in the wild. In chapter two I tested for the action of parasite mediated balancing and divergent selection on on MHC loci using naturally infected stickleback in three replicate lake-stream pairs. Despite consistent divergence in parasites and MHC alleles, lakes tended to show decreased parasite burdens with increased allelic richness (consistent with balancing selection), while streams showed some support for divergent selection between lake and stream types. In chapter three I use the same lake-stream pairs to investigate how divergent selection could instead be reflected in variation in the effects of individual MHC alleles among populations. When comparing parapatric populations experiencing gene flow, MHC alleles maintained at relatively high frequency in one population were more likely to be associated with reduced, rather than increased, parasite abundances in that population. Allopatric populations experiencing no gene flow showed no such general relationship between allele frequency and resistance. These results are only consistent with spatially divergent selection, and imply that gene flow and environmental heterogeneity can be important for maintaining MHC diversity. / text