Botrytis cinerea (anamorph of Botryotinia fuckeliana) is a filamentous ascomycete that causes grey mould especially on grapevine. Based on the presence or the absence of two transposable elements (Boty and Flipper) two sibling sympatric populations named transposa and vacuma have been described. Among the vacuma population, some strains (designated HydR1) were found to be resistant to fenhexamid (a sterol C-4 demethylase inhibitor) and to show an increased sensitivity to 14α-demethylase inhibitors (DMIs). In order to assess whether or not mutations at the target gene level (CYP51) could underlie increased sensitivity to DMIs in HydR1 strains, we cloned the CYP51 gene and determined its DNA sequence in various B. cinerea strains. The gene was highly polymorphic, with mutations detected at 58 positions in the 35 strains analysed. The polymorphisms did not discriminate between transposa and vacuma strains, but did distinguish between HydR1 and non-HydR1 ones. Two expressed mutations were present in all HydR1 strains, namely phenylalanine to leucine at position 15 of the inferred protein, and serine to asparagine at position 105. These data, combined with the existence of morphological differences and somatic incompatibility between HydR1 and non-HydR1 strains, suggest that these two groups comprise distinct genetic entities.