Grey mould is a worldwide disease on many economically important crops. It is caused by two fungal species, Botrytis cinerea and B. pseudocinerea, which are mainly airborne dispersed. Although several studies have considered the abundance of airborne inoculum of B. cinerea in models forecasting the risk of grey mould epidemics, the genetic characteristics of this inoculum are poorly known. In the present study, airborne inoculum of B. cinerea and B. pseudocinerea was collected on 29 dates over a 2.5-year period on a site in south-eastern France. The 683 sampled isolates were genotyped with nine microsatellites markers, and 616 were identified as B. cinerea. The genetic structure of B. cinerea airborne inoculum was inferred with Bayesian assignment tests. Eight genetic clusters were identified. Cluster abundance showed temporal variation and was statistically linked to the season (P = 0.0009) and the origin of air masses (P < 0.0001). The proportion of isolates belonging to the species B. pseudocinerea was equal to 9.8 % on average, but it showed temporal variation; it tended to be higher in winter. This study is the first to provide information about the genetic characteristics of airborne inoculum of B. cinerea and B. pseudocinerea and to bring evidence of relationship with seasons, meteorological parameters and with the origin of air masses.