Little was known about the small mammal fauna of the Marcal Basin to date, therefore we collected 1,144 Barn Owl pellets from 15 locations in 2017. After the analysis of the pellets, remnants of 3,063 prey items were identified, of which 97.5% were small mammals, belonging to 21 species, while the remaining 2.5% were birds, frogs and insects. Mammal prey items consisted of Cricetidae 41%, Muridae 31% and Soricidae 28%, and in some samples, we found the remnants of European Mole (Talpa europaea), Kuhl’s Pipistrelle (Pipistrellus kuhlii), Hazel Dormouse (Muscardinus avellanarius) and Least Weasel (Mustela nivalis). Small mammal species were classified into four functional groups based on their preferences for urban, open, forest or wetland habitats. We investigated whether their relative abundances match with the proportions of the four habitat types in the assumed Barn Owl hunting ranges (cca. 2 km radius circle) in five sample sites. The relative abundance of small mammal species preferring urban habitats showed concordance with the proportion of the appropriate habitat types in the hunting area in two samples, while such concordance was proved for species favouring open, forest and wetland habitats just in one out of five samples. Small mammal functional groups represented in the prey composition do not directly correspond to the proportion of their typical habitats. We conclude that the abundance of various prey types is not suitable for characterising the landscape within the Barn Owl’s hunting range.