The incidence of garlic rot has constantly increased in France since the early 2000s. To set up an efficient method of garlic protection against this disease, we have clarified the etiology of this disease. This was achieved by surveying garlic from the two main French basins of garlic production during 3 years. Fungi were isolated from 5493 garlic cloves belonging to pink, purple and white garlic types. Sequencing of the translation elongation factor 1 alpha gene of 1171 strains revealed that 94 % of the strains belong to the species Fusarium proliferatum and 6 % belong to F. oxysporum. The pathogenicity of both species on garlic was confirmed by artificial inoculations and re‐isolations. There was significantly more F. oxysporum in symptomatic garlic cloves coming from the southeast basin (9.44 %) than from the southwest basin (2.76 %). This study confirms that garlic rot is present in pink, purple and white types. However, pink type garlic harbors F. oxysporum significantly less frequently (1.59 %) than do white (9.39 %) and purple (7.34 %) types. Sequencing of rpb1, rpb2, ITS and IGS regions of a subsample of strains revealed that there is little genetic diversity of the French population of F. proliferatum.