In small planktonic organisms, large census sizes (Nc) suggest large effective population sizes (Ne), but reliable estimates are rare. Here, we present Ne/Nc ratios for two freshwater copepod species (Eudiaptomus sp.) using temporal samples of multilocus microsatellite genotypes and a pseudo-likelihood approach. Ne/Nc ratios were very small in both Eudiaptomus species (10−7–10−8). Although we hypothesized that the species producing resting eggs (E. graciloides) had a larger Ne than the other (E. gracilis), estimates were not statistically different (E. graciloides: Ne = 672.7, CI: 276–1949; E. gracilis: Ne = 1027.4, CI: 449–2495), suggesting that the propagule bank of E. graciloides had no detectable influence on Ne.