Diapausing egg banks are reservoirs of ecological and genetic diversity in continental zooplankton. However, although habitat size has often been used as a proxy for population size, the relationship between diapausing egg bank size and genetic diversity has not been explicitly tested in zooplankton. We estimated the density and size of diapausing egg banks, habitat size and genetic diversity (for mitochondrial and nuclear markers) of 14 populations of the rotifer Brachionus plicatilis in an endorheic basin in the SE Iberian Peninsula. The size of B. plicatilis diapausing egg banks ranged across eight orders of magnitude (from 257 to 4.9 × 1010 eggs). Despite the small geographical scale, populations were strongly structured genetically, but with no evidence of isolation by distance. Habitat size (lake area) was a better predictor of genetic diversity than total diapausing egg bank size, but only for mtDNA haplotype diversity. However, as these results were driven by the strong effect of the largest lake in the database, they should be taken with caution. Our results suggest that large lakes could have a disproportionate effect on genetic diversity and that more work is needed to support the use of habitat size as a proxy of population size in rotifers.