A new freshwater benthic diatom genus, Microfissurata gen. nov., was identified from light and scanning electron micrographs. The most characteristic morphological feature (referred to also by the name of the new genus) is the structure of the striae/alveoli, which are simple, mostly uninterrupted, transapical slits. The combination of characteristics of the new genus is unique. It includes two new species: Microfissurata paludosa Cantonati et Lange-Bert. sp. nov. and M. australis Van de Vijver et Lange-Bert. sp. nov., distributed in Europe and on an austral island, respectively. The new genus occurs in freshwater dystrophic lakes, pools, seepage springs, mires, and in intermittently wet terrestrial habitats. It is not abundant but widespread wherever these habitat types are well developed, in Nordic-alpine and sub-Antarctic areas. Overall, the new genus appears to be mostly epiphytic (bryophilous) and capable of tolerating a wide range of moisture conditions (xerotolerant). The finding of the type species (M. paludosa) in a well-investigated area like central Europe highlights the diatom species richness of dystrophic habitats and their importance for diatom biodiversity conservation.