The structure of a population over time, space and categories of social and sexual role governs its ability to retain genetic variation in the face of drift. A metapopulation is an extreme form of spatial structure in which loosely coupled local populations ‘turnover’, that is, suffer extinction followed by recolonization from elsewhere within the metapopulation. These local populations turn over with a characteristic half-life. Based on a simulation model that incorporates both realistic features of population ecology and population genetics, the ability of such a metapopulation to retain genetic variation, which may be defined as proportional to its so-called effective population size, denoted Ne(meta), can be one to two orders of magnitude lower than the maximum total number of individuals in the system. Ne(meta) depends on the persistence time associated with longevity of local populations (the turnover half-life), the average number of local populations extant in the metapopulation and the gene flow between local populations. Habitat fragmentation, which can create a metapopulation from a formerly continuously distributed species, may have unappreciated large genetic consequences for species impacted by human development.