Genomes vary in diversity within and among species. Even within diploid individuals, there are parts of the genomes that are characterized by high diversity (heterozygosity) and others that are more homozygous. It is the aim of this talk to discuss how such differences come about and are maintained in natural free-living populations. I will give a brief back ground on recombination and linkage disequilibrium. I will then describe a genomic region described as a recombinatiopn ‘hotspot‘ with examples of our studies of the MHC-region in the black grouse (Tetrao tetrix). Next I will discuss a recombination ‘coldspot‘: an inversion polymorphism (so called supergene) recently discovered in the ruff (Philomachus pugnax) which may explain the maintenance of the extraordinary behavioural polymorphism found in males of this species. I will end by relating our findings to other studies of supergenes and the maintenance of complex phenotypic traits.