The community composition and structure of helminths of Pipistrellus pipistrellus (Schreber, 1774) from two widely separated Spanish localities, El Saler (n = 42) and the San Pedro pothole (n = 34), were determined and compared. Five species of trematodes, Plagiorchis (Plagiorchis) sp., Lecithodendrium (Lecithodendrium) linstowi Dollfus, 1931, Prosthodendrium (Prosthodendrium) sp., Pycnoporus heteroporus (Dujardin, 1845) and Parabascus semisquamosus (Braun, 1900), and one species of cestode, Hymenolepis pipistrelli López-Neyra, 1941, were found. The two bat populations harboured the same helminth species and showed the same trematode dominance, but the most important differences between the two helminth community structures were attributable to L. (L.) linstowi and H. pipistrelli. The mean species richness in the two localities was not significantly different. The mean number of helminth species per infected bat, mean infracommunity abundance and mean infracommunity diversity showed significant differences between both localities. The number of helminths per bat in both populations displayed an aggregated distribution. Results indicate that the different characteristics of the P. pipistrellus foraging area in both localities are important in determining the composition and structure of helminth communities in this bat species. This is the first study of a Palaearctic bat helminth community.