Many species exist as metapopulations in balance between local population extinction and recolonization, processes that may strongly affect the distribution of neutral genetic diversity within demes and in the metapopulation as a whole. In this paper we use both the infinite-alleles and the infinite-sites models to reframe Slatkin's propagule-pool and migrant-pool models in terms of mean within-deme and among-deme genetic diversity; the infinite-sites model is particularly relevant to DNA sequence data. Population turnover causes a major reduction in neutral genetic diversity within demes, pi(S), and in the metapopulation as a whole, pi(T). This effect is particularly strong for propagule-pool colonization, in which colonists are drawn from a single extant deme. Because metapopulation dynamics affect both within-deme and total metapopulation diversity similarly, comparisons between species with different ecologies on the basis of ratios such as F-ST are difficult to interpret and absolute measures of divergence between populations should be used as well. Although the value of F-ST in a metapopulation with local extinction depends strongly on the mode of colonization, this has almost no effect on the numerator of the F-ST ratio, pi(T) - pi(S), so that F-ST is influenced mainly by the effect of the colonization mode on the denominator (pi(T)). Our results also indicate that it is inappropriate to use measures of average within-deme diversity in species with population turnover to estimate the scaled mutation rate, theta, because extinction can greatly reduce pi(S). Finally, we discuss the effect of population turnover on the effective size of a metapopulation.