Although Botrytis cinerea is known for its ability to produce high amounts of spores on diseased plants, enabling it to complete rapidly numerous developmental cycles in favorable environments, population genetics studies of this fungus indicate enormous diversity and limited clonal spread. Here, we report an exception to this situation in the settings of commercial tomato greenhouses. The genotypic characterization of 712 isolates collected from the air and from diseased plants, following the development of gray mould epidemics in four greenhouses in Southern France, revealed the presence of a few predominant genotypes in a background of highly diverse populations. The comparison of genotypic profiles for isolates collected in the air or on the plants was compatible with the entry in the greenhouse of substantial amounts of inoculum from the outside environment, but it also highlighted the importance of secondary inoculum produced within the crop. The overall results of this work suggest that sporulation could be thus an important target for disease management strategies in the greenhouse.