A new diatom species from freshwater environments in France is described. Fragilaria microvaucheriae sp. nov. is illustrated and discussed based on populations from the Loire-Brittany basin and compared with the original (type) material of Fragilaria vaucheriae (Kütz.) J.B.Petersen (= Exilaria vaucheriae Kütz.) from Germany and Fragilaria uliginosa Kulikowskiy et al., recently described from a peat bog in Mongolia. Additional populations of Fragilaria pectinalis (O.F.Müll.) Lyngb. from the Rhône Alpes region (France) are also investigated in detail including its environmental preferences in order to compare with the new species. Fragilaria microvaucheriae is similar to F. vaucheriae but present smaller cell dimensions and higher density of striae. It occurs in slight acidic waters. The new species has been identified in the past as F. vaucheriae, Fragilaria capucina sensu auct., Fragilaria austriaca (Grunow) Lange-Bert. or Fragilaria pectinalis. The morphology of the new species and similar taxa is documented by light (LM) and scanning electron micrographs (SEM) and discussed in light of recent advances in the taxonomy of the genus Fragilaria Lyngb. from freshwater environments.