The endangered Euphrates soft-shelled turtle, Rafetus euphraticus, is endemic to the Mesopotamian River Basin in the Middle East. Within recent decades, populations of this aquatic species have been heavily depleted and severely fragmented owing to habitat alteration and destruction by drainage and hydroelectricity dam constructions. Continuing habitat loss and fragmentation are considered the main drivers for the population decline of R. euphraticus.Intraspecific genetic variability was investigated using two mitochondrial gene fragments for 31 specimens covering most of the distributional range of the species. Habitat suitability models were computed using a combination of bioclimatic and remote sensing variables as environmental predictors to assess habitat suitability, habitat fragmentation and coverage by designated protected areas across the range of R. euphraticus.Beyond single substitutions in two sequences, no significant genetic variation could be detected in R. euphraticus. Models show habitat suitability to be high throughout the range of the species, although only a fraction is currently covered by reserves. Habitat suitability and coverage of reserves is highly variable among countries. South-western Iran appears to be of major importance for future conservation strategies. Suitability models are in concordance with the habitat selection patterns of R. euphraticusThe existing reserve system is considered insufficient and has to be significantly improved in order to sustain viable populations of R. euphraticus. To counter continuing fragmentation and alteration by dam construction, future conservation measures should focus on highlighted priority areas. Copyright (c) 2014 John Wiley & Sons, Ltd.