Genetic markers have helped to resolve many difficult taxonomic problems and map patterns of diversity within and among remnant populations of threatened and endangered species. Knowledge of historical patterns of gene flow can help to manage dispersal among anthropogenically fragmented populations. Genetic considerations are used in the design of captive breeding programmes that avoid inbreeding depression and artificial selection that may impact on Darwinian fitness. Case studies from endangered populations of topminnows from North American deserts are used to illustrate a variety of methods used in conservation genetic studies. Several merits of studying putatively neutral, molecular markers v. adaptive phenotypic traits are discussed.