Founder effects introduce stochasticity in the genetic structure of species at the regional scale. To the extent that founder effects are important, they will result in a reduced signature of space, time, and environmental variation in landscape genetic data. We studied the metapopulation genetic structure of recently founded populations of the microcrustacean Daphnia sinensis in 10 Ethiopian water reservoirs. We used three different approaches to estimate the number of effective founders and applied them to two independent genetic marker sets in an effort to investigate the role of founder effects and to estimate effective size of the founding population. Estimates of founding sizes rarely exceeded eight individuals but were most often limited to less than four individuals. No associations of genetic identities, gene frequencies, measures of genetic diversity, or differentiation with environmental and spatial variables were found. Age and size of the reservoirs were not correlated with genetic diversity measures or number of founders in these reservoirs. These findings indicate that neither strong selection, nor dispersal limitation are responsible for the observed pat- tern of genetic variation. Our results suggest a regional population structure that is strongly impacted by founder events, reflecting colonization by just a few founders per waterbody, and not noticeably influenced by subsequent dispersal and gene flow. Our results show that rapid colonization of empty habitats and fast population growth by a handful of founders can result in strong founder effects, even in relatively large habitats that are likely regularly reached by new immigrants.