Despite the lesser preservation of bat fossils compared to karstic sites, fluvio-lacustrine deposits are of crucial importance for assessing the local palaeodiversity of bats. This is confirmed by three faunas from the Late Miocene of Slovakia (Borský Svätý Jur, MN9; Studienka A, MN9; Krásno, MN11), which comprise seven species (Miostrellus noctuloides, Myotis cf. M. murinoides, cf. Submyotodon sp., Eptesicus cf. E. campanensis, Vespertilionidae gen. sp. indet. 1, Vespertilionidae gen. sp. indet. 2, Rhinolophus cf. R. grivensis). Bats represent approximately 1.47% of the small mammal remains from Borský Svätý Jur, approximately 0.25% of those from Studienka A and approximately 1.87% of those from Krásno. The MN11 fauna from Krásno consists of five distinct species, which is unusual for a Miocene-aged fluvio-lacustrine deposit. Most likely, this is the consequence of the relatively high frequency of bats in the taphocoenosis, therefore providing a more complete and more accurate picture of the Carpathian Late Miocene bat faunas. This material encourages the study of fluvio-lacustrine deposits to unravel the cryptic diversity of Neogene taxa.