METAPOP (http://webs.uvigo.es/anpefi/metapop/) is a desktop application that provides an analysis of gene and allelic diversity in subdivided populations from molecular genotype or coancestry data as well as a tool for the management of genetic diversity in conservation programs. A partition of gene and allelic diversity is made within and between subpopulations, in order to assess the contribution of each subpopulation to global diversity for descriptive population genetics or conservation purposes. In the context of management of subdivided populations in in situ conservation programs, the software also determines the optimal contributions (i.e., number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of individuals in order to maintain the largest level of gene diversity in the whole population with a desired control in the rate of inbreeding. The partition of gene and allelic diversity within and between subpopulations is illustrated with microsatellite and SNP data from human populations.