A new freshwater diatom species was described from southwest Europe (Portugal), based on morphological and ultrastructural characteristics. Fragilaria misarelensis Almeida, C.Delgado, Novais & S.Blanco is characterised by lanceolate valves, with slightly capitate ends, alternate striae and lacking spines joining adjacent cells, which are solitary. The valve shape of Fragilaria misarelensis, when compared to similar forms, is unique, as revealed by a thorough literature survey of Fragilaria species, geometric morphometry and discriminant analysis. Fragilaria misarelensis sp. nov. was frequent and abundant in central Portugal, in poorly mineralized watercourses under low anthropogenic influence, characterised by neutral pH, low conductivity and high dissolved oxygen concentration. The analysis of type material belonging to similar species, Fragilaria capucina fo. sublanceolata-baikali, F. capucina fo. lanceolata-baikali and F. nevadensis, contributed to improving their characterisation and illustration, also supporting the delimitation of the new Portuguese species. Fragilaria capucina fo. sublanceolata-baikali and F. capucina fo. lanceolata-baikali were considered to differ substantially from F. capucina and raised to species level as Fragilaria sublanceolata-baikali (Flower & D.M.Williams) Novais, C.Delgado & S.Blanco, comb. et stat. nov. and Fragilaria lanceolata-baikali (Flower & D.M.Williams) Novais, C.Delgado & S.Blanco, comb. et stat. nov.