This paper describes, as a part of the resistance risk assessment, the genetic analyses which were performed to evaluate the resistance risk of the phenylpyrrole fungicide fludioxonil and the implications for cross resistance with the dicarboximide vinclozolin. Cross resistance between dicarboximides and phenylpyrroles, often found in the laboratory, has been extremely rare in the field. Over seven years of monitoring in Switzerland no fludioxonil field resistant isolates were found. Sexual crosses between a fludioxonil field resistant/vinclozolin field resistant strain isolated in France and a sensitive one showed an independent segregation of the resistance to the two fungicides, suggesting that different genes regulate field resistance to fludioxonil and vinclozolin. Sexual crosses between a fludioxonil field resistant B. fuckeliana strain and a fludioxonil laboratory resistant strain indicated that the two fludioxonil resistance phenotypes segregate independently. We concluded that fludioxonil resistance is influenced by at least two different genes. Genetic studies with laboratory strains resistant to both fungicides demonstrated a low segregation rate between fludioxonil and vinclozolin resistant phenotypes. These results let us hypothesize that fludioxonil and vinclozolin resistance induced in laboratory could be due to two genes closely linked. Finally, pathogenicity tests performed with progenies of sexual crosses showed a positive correlation between virulence and phenotypes.