Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable outcrossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.