There are more than 70 known unisexual species of fishes, amphibians, and reptiles. They are all-female populations of interspecific hybrid origin that reproduce without sex via altered gametogenetic mechanisms. They are either sperm independent as in parthenogenesis or sperm dependent as in gynogenesis or hybridogenesis, which causes clonal (or hemiclonal) inheritance. The first two modes of reproduction produce species composed of genetically isolated clones. In many previous papers, origin and ancestry, clonal diversity based on allozyme or mitochondrial DNA variation, ecology and evolution of unisexual vertebrates were discussed. This chapter reviews the role of mutations in genome diversity of some unisexual vertebrates revealed by DNA fingerprinting and/or by locus-specific PCR. It also describes recent data on molecular structure of unstable microsatellite loci and their allelic variants in parthenogenetic lizard species. The available data demonstrate that microsatellite mutations as well as point mutations in flanking regions make significant contribution in genome diversity of, at least some, clonaly reproduced vertebrates.