Variability of Botrytis species (26 isolates of Botrytis fabae and 3 isolates of B. cinerea) representing different geographical regions cultivated with faba bean in Egypt was studied. Phenotypic variation between isolates of the fabae sp. (sporulation less than 18.1 X 10 6 / plate) compared to the cinerea sp. (sporulation more than 19.5 X 10 6 / plate) was found. The fabae sp. produced small sized sclerotia in large number, while the cinerea sp. either did not produce sclerotia or produced large sized sclerotia but less in numbers than the fabae sp. The most virulent isolates were 28 and 29 of fabae sp that showed disease severity of 5.1 and 5.7, respectively. These isolates were obtained from Noubaria region. However, the less virulent isolates were of the cinerea sp. and were isolated from plants grown in Nubaria, Dakahlia and Kafr El-Sheikh regions. Other isolates showed intermediate reaction in their virulence. Primer pairs Bc 6 (r & f) amplified a single band at 90 bp for all Botrytis fabae isolates except isolate no.4 which was isolated from Nubaria that did not react positively. Botrytis cinerea produced polymerase chain reaction (PCR) products at 120 bp.On the other hand, primer pairs Bc 9 (r & f) amplified a single band of 90 bp for all Botrytis fabae isolates except isolates isolated from Nubaria region (isolates no. 4 and 7). Botrytis cinerea produces PCR product at the same size(90 bp) of Botrytis fabae isolates. Finally, primer BC6 was the best in differentiating between Botrytis fabae and Botrytis cinerea isolates.