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We examined the rotifer community composition in 130 freshwater Mediterranean ponds which included a wide range of limnological characteristics. The objective was to test the effectiveness of rotifer assemblages in the identification of different ponds types and the forcing factors that determine their distribution. Among the environmental variables analysed hydroperiod stands out as a major factor separating true temporary ponds from those with permanent water stability. Abiotic and biotic factors showed a different relative importance in the two groups of ponds. Among the temporary ponds, abiotic variables, such as arid climate, turbidity and short hydroperiod defined a special group called argillotrophic, in which Rhinoglena frontalis was found to be the most characteristic rotifer species. Those temporary ponds with short hydroperiods supported few species (mean species richness 4) and, in the main, planktonic species. Permanent ponds supported higher species richness (mean 13 and maximum 33 species) composed mainly of littoral species. The rotifer community of permanent ponds was found to be correlated with biotic factors, such as fish and macrophyte abundance. High macrophyte cover favours complex habitat heterogeneity and a wider range of feeding traits, ranging from algae-grazing species to carnivorous species (Dicranophorus grandis or Cupelophagis vorax). These results showed that rotifer communities are useful to provide a typology of ponds with a hierarchical order of factors structuring them ranging from abiotic to biotic factors. This is an example of Stress Gradient Hypothesis being more significant in the heterogeneous Mediterranean area, and which may indicate trends of changes related to the conservation status or the effects of global warming.