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The dataset contains records of bats (Chiroptera) collected in the lower valley of River Tua. Data were collected in the scope of the long-term Ecological Monitoring Program (PME) and the Monitoring Program of Mitigation/Compensation Measures (PMC) of the Foz Tua Hydroelectric Dam, promoted by EDP – Energias de Portugal, S.A. Data were collected between July 2011 and September 2017 during field visits to 91 known or presumed bat hibernation, reproduction and pre-dispersion (post-reproduction) roosts, within a 5-km radius buffer around the lower valley of River Tua. From 2012, two roosts located at >20 km from the river (deactivated railroad tunnels) were added to the sampling sites in the context of the PMC. The presence of individuals was recorded by direct observation, and all individuals were photographed whenever possible. The records include taxa identified at the species or genus level. In several occasions it was not possible to separate the individual species, so they were grouped in 15 “species complexes”, both mono-specific and multi-specific. Due to the vulnerability of the roost locations, the precision of the geographic coordinates was degraded to 0.01, according to the recommendations of Chapman & Grafton (2008). The dataset with the original (undegraded) coordinates may be provided upon request by the resource contact from EDP, who will define the terms and conditions for its use.