1. Species distribution modelling can be useful for the conservation of rare and endangered species. Freshwater mussel declines have thinned species ranges producing spatially fragmented distributions across large areas. Spatial fragmentation in combination with a complex life history and heterogeneous environment makes predictive modelling difficult. 2. A machine learning approach (maximum entropy) was used to model occurrences and suitable habitat for the federally endangered dwarf wedgemussel, Alasmidonta heterodon, in Maryland's Coastal Plain catchments. Landscape- scale predictors (e. g. land cover, land use, soil characteristics, geology, flow characteristics, and climate) were used to predict the suitability of individual stream segments for A. heterodon. 3. The best model contained variables at three scales: minimum elevation (segment scale), percentage Tertiary deposits, low intensity development, and woody wetlands (sub- catchment), and percentage low intensity development, pasture/ hay agriculture, and average depth to the water table (catchment). Despite a very small sample size owing to the rarity of A. heterodon, cross- validated prediction accuracy was 91%. 4. Most predicted suitable segments occur in catchments not known to contain A. heterodon, which provides opportunities for new discoveries or population restoration. These model predictions can guide surveys toward the streams with the best chance of containing the species or, alternatively, away from those streams with little chance of containing A. heterodon. 5. Developed reaches had low predicted suitability for A. heterodon in the Coastal Plain. Urban and exurban sprawl continues to modify stream ecosystems in the region, underscoring the need to preserve existing populations and to discover and protect new populations. Copyright # 2016 John Wiley & Sons, Ltd.