P>1. Changes in cladoceran subfossils in the surface sediments of 54 shallow lakes were studied along a European latitude gradient (36-68 degrees N). Multivariate methods, such as regression trees and ordination, were applied to explore the relationships between cladoceran taxa distribution and contemporary environmental variables, with special focus on the impact of climate. 2. Multivariate regression tree analysis showed distinct differences in cladoceran community structure and lake characteristics along the latitude gradient, identifying three groups: (i) northern lakes characterised by low annual mean temperature, conductivity, nutrient concentrations and fish abundance, (ii) southern, macrophyte rich, warm water lakes with high conductivity and high fish abundance and (iii) Mid-European lakes at intermediate latitudes with intermediate conductivities, trophic state and temperatures. 3. Large-sized, pelagic species dominated a group of seven northern lakes with low conductivity, where acid-tolerant species were also occasionally abundant. Small-sized, benthic-associated species dominated a group of five warm water lakes with high conductivity. Cladoceran communities generally showed low species-specific preferences for habitat and environmental conditions in the Mid-European group of lakes. Taxon richness was low in the southern-most, high-conductivity lakes as well as in the two northern-most sub-arctic lakes. 4. The proportion of cladoceran resting eggs relative to body shields was high in the northern lakes, and linearly (negatively) related to both temperature and Chl a, indicating that both cold climate (short growing season) and low food availability induce high ephippia production. 5. Latitude and, implicitly, temperature were strongly correlated with conductivity and nutrient concentrations, highlighting the difficulties of disentangling a direct climate signal from indirect effects of climate, such as changes in fish community structure and human-related impacts, when a latitude gradient is used as a climate proxy. Future studies should focus on the interrelationships between latitude and gradients in nutrient concentration and conductivity.