During a biomonitoring assignment in the Swiss canton Ticino, an unknown Fragilaria taxon was discovered that could not be identified using the currently available literature. The results of a morphological comparison with the type material of F. recapitellata, based on light and scanning electron microscopy, showed that the new Swiss taxon has sufficient differences to be separated as a new species: Fragilaria subrecapitellata sp. nov. The new species can be separated by its lanceolate to elliptic-lanceolate valve outline with convex valve margins, and its smaller valves compared to F. recapitellata. The distribution and iconography of F. recapitellata in literature data is analysed. As a result of this analysis, Fragilaria deformis is appointed as the correct name for the taxon generally known as F. candidagilae or F. capucina var. capitellata (Grunow) Lange-Bertalot in Krammer & Lange-Bertalot.