In addition to variations on the spatial scale, short- and long-term temporal variations, too, can impose intense selection on the overall genetic diversity and composition of a population. We hypothesized that the allelic composition in populations of the eastern spadefoot toad (Pelobates syriacus) would change among successive years in accordance with the short-term changes in environmental conditions. Surprisingly, the effect of short-term climate fluctuations on genetic composition have rarely been addressed in the literature, and to our knowledge the effect of annual climatic fluctuations have not been considered meaningful. Our findings show that climatic variation among successive years, primarily the amount of rainfall and rainy days, can significantly alter both microsatellite allelic composition and diversity. We suggest that environmental (i.e. fluctuating) selection is differential across the globe, and that its intensity is expected to be greatest in regions where short-term climatic conditions are least stable.