The publication of the handbook of European freshwater fishes by Kottelat and Freyhof in 2007, in which the authors list 16 additional native species in France, set off a taxonomical revision of French and European ichthyofauna. The objective of the present thesis is to revise 5 genera of freshwater fishes of France in an integrative taxonomy framework using morphological, molecular and ecological data: Squalius (chub), Phoxinus (minnow), Gobio (gudgeon), Esox (pike) and Gasterosteus (three-spined stickleback). More than 600 lots were collected in 283 locations in France and studied morphologically, before integration in the MNHN collections. More than 900 specimens were studied genetically, including complete mitogenome sequencing for a subset. Also we compared secondary sexual ornamentation of minnows among basins, as well as an analysis of the niches occupied by the different gudgeon species. The results confirm the presence of two chub species in France S. cephalus and S. laietanus. The use of molecular data invalidates G. gymnurus, so there is a single species of three-spined stickleback G. aculeatus. The study of collection material shows the presence of three pike species: E. lucius, E. cisalpinus and a previously undetected new species E. aquitanicus. Secondary sexual ornamentation corroborated by sequence data discriminates 6 minnow species, including P. phoxinus, P. bigerri, P. septimaniae, P. marsilii which would be valid, as well as two new species. The use of morphological, molecular and ecological data support 3 out of the 4 gudgeon species (G. gobio, G. lozanoi and G. occitaniae; G. alverniae would be a junior synonym of G. occitaniae). The new taxonomical data highlight the gaps in our knowledge of the French freshwater fauna. It opens new perspectives and opportunities of research in numerous fields of biology. However this kind of in-depth study should be applied to all French taxonomic groups.