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Organisms adapted to ephemeral habitats often display striking variation in population size owing to environmental stochasticity, Here we investigate the genetic consequences of demographic variation in Eichhornia paniculata (Pontederiaceae), an annual tristylous aquatic that inhabits ephemeral pools, ditches, and low-lying pastures in the seasonally arid caatinga region of northeast Brazil, Annual censuses of populations demonstrated striking temporal variation in census number, There was no association between population size and heterozygosity at allozyme loci, but a significant positive relation was evident with the harmonic mean of population size, Both population-size measures were positively associated with style-morph diversity, Large populations were more likely to contain the three style morphs at similar frequencies than small, The amount of heterozygosity within populations was positively correlated with the local density of populations in a region, presumably reflecting greater opportunities for gene flow, Bottlenecks in population size were not severe enough to reduce genetic variation, and population persistence versus local extinction was unrelated to the amount of allozyme variation within populations. The demographic and genetic characteristics of ephemeral populations may be largely irrelevant to survival where catastrophic changes to local environments through drought, flooding, and human disturbance often occur.