Studying the population genetics of the Y chromosome is the most simple and direct way to gain independent information on male-specific historic and contemporary evolutionary processes. Y-chromosomal polymorphisms can now be accessed thanks to recent developments in cytogenetic technologies, thus allowing the direct study of male population genetics. More interestingly, because males are the heterogametic sex in mammals, the use of both Y-specific and mitochondrial polymorphisms with autosomal loci offers a unique opportunity to infer sex-specific population parameters and to explore crucial aspects of both breeding systems and dispersal strategies.