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1. The relationship between altitudinal gradients on small spatial scales and latitudinal gradients on broader scales has been repeatedly recognised in the biogeography of animals and plants. However, little is known about this topic in the ecology and biogeography of ostracod communities in Mediterranean flowing waters or the factors underlying these spatial patterns. 2. We analysed the ostracod assemblages of near-natural headwater streams in the Betic and Pre-Betic Mountains in the southern Iberian Peninsula to decipher the most important environmental gradients structuring ostracod communities on a local scale. In addition, the European altitudinal and latitudinal distributions of the most commonly found species were analysed with GIS and regression models to compare geographical effects from local to continental scales. 3. Forty sampling sites, distributed among six catchments and ranging in altitude between 150 and 1940 m a.s.l., were sampled seasonally. Limnological and geographical information was also recorded for each sample. Seventeen ostracod species were found, two of which were new findings for the Iberian Peninsula: Potamocypris fulva and Cypria reptans. The most common species were Potamocypris zschokkei, Candona neglecta, Herpetocypris brevicaudata, Cyclocypris ovum, Potamocypris villosa and Pseudocandona albicans. The distribution of these species in 918 European locations was analysed to test the hypothesised change in altitudinal distribution with varying latitude. 4. The best subset of logistic and linear regression models, selected by means of the information-theoretic approach, found that oxygen content and the variables related with substratum and discharge were the most important variables with a negative influence on ostracod presence, abundance and species richness on a local scale. These findings suggest that the negative effect on benthic invertebrates of physical disturbances relates to high flow velocity and turbulences. 5. Multivariate ordination methods show how altitude and water chemistry are the most important variables to explain the distribution of ostracod assemblages on the small spatial scale. On a larger scale, differences in latitudinal distribution throughout Europe were significant for the six most common species found in Granada. In addition, four of these showed significant negative linear relationships between latitude and altitude in Europe, supporting the important effect of climate on local and continental scale distributions. While ostracod biogeographies are still poorly known, our results indicate the influence of Quaternary climate variability on ostracod dynamic colonisation and extinction in Europe in accordance with species-specific temperature and water chemistry preferences. [ABSTRACT FROM AUTHOR]