The necrotrophic fungus Botrytis cinerea, known as the causal agent of gray mold, is ranked second for its phytopathological global-impact. The disease is controlled by cultural means and fungicides, however, these techniques have variable effect on different fungal isolates due to the plasticity of the pathogen populations. Here we studied and characterized the genetic and virulence associated variability of B. cinerea isolates from different sources. Starting from initial survey of 31 B. cinerea isolates, collected from seven hosts in different locations of Israel, we have focused on 10 isolates that exhibited potential phytopathogenic variability. Two genetic markers (microsatellite) Bc1 and Bc7, were able to differentiate between these isolates. Our analysis demonstrates significant variability in saprophytic growth rate, necrotrophic growth rate on tomato leaves and stems, and in the incidence of infection on leaves of whole plants. Following the observation of significant correlation between saprophytic growth rate, and necrotrophic growth on leaves, we have studied normalized (by saprophytic growth) virulence. Utilization of normalized necrotrophic growth rate enabled to indicate on the presence of virulence mechanisms other than growth rate, for several isolates. Exploration of this direction illustrated variability in resistance to paraquat (associated with resistance to oxidation), which was associated with high and low superoxide dismutase (SOD) gene expression for selected isolates showing high or low paraquat resistance, respectively. Finally, we have used unsupervised learning (clustering analysis) to explore patterns in the multivariable space, which demonstrated two modes of pathogenicity in the tested B. cinerea isolates.