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The hyperarid region of Israel and Jordan covers a large area where numerous sites of Pleistocene lake sediments suggest that climate conditions were significantly wetter during the Pleistocene. This region experienced a significant increase in aridity in recent decades and the number of existing surface waters is diminishing rapidly. We studied ostracod shells from 49 pond and stream sites to determine the species distribution and to infer ecological preferences especially with respect to general differences in water movement, conductivity and ion composition. Twenty-two ostracod species were identified in total of which 12 taxa occur at three or more sites. Among the rarer species. Cyprinotus scholiosus was identified for the first time after two records from Plio- and Pleistocene sites in Yemen and Saudi Arabia. Further, Paracypretta amati was recorded and its ecological preferences discussed for the first time following the description of the species from its type locality in Sudan. Cypridopsis elongata is the only typical inhabitant of lotic habitats, strictly preferring freshwater conditions and waters with an alkalinity/Ca ratio around 1 and cations dominated by Ca(2+) and anions by HCO(3)(-). In contrast, Cyprideis torosa, Limnocythere inopinata and Heterocypris incongruens apparently prefer waters dominated by Na(+) associated with cations and Cl(-) associated with anions. Heterocypris salina and C. torosa occur over a wide conductivity (or salinity) range and in waters with alkalinity/Ca ratios around 1 and with significant alkalinity depletion. Humphcypris subterranea, Ilyocypris spp. and H. sauna are the only taxa which do not show any preference with respect to both the cation and anion dominance of the waters. The ecological preferences of the ostracod species from water bodies in the study area are discussed in detail and can be used for a qualitative assessment of the hydrodynamical and hydrochemical conditions of former water bodies in the presently hyperarid environment based on ostracod species composition analysis of Pleistocene aquatic sediments. (C) 2011 Elsevier Ltd. All rights reserved.