Two cysteine proteinase genes of the papain family, NbCYP1 and NbCYP2, were amplified from cDNA of Nicotiana benthamiana leaves infected with the hemibiotrophic fungus Colletotrichum destructivum. Both genes showed peak expression corresponding with the switch from biotrophic to necrotrophic growth by C. destructivum at 72 h post-inoculation (HPI). For N. benthamiana inoculated with the incompatible bacterium, Pseudomonas syringae pv. tomato, expression of NbCYP1 significantly decreased at 12 HPI, whereas NbCYP2 expression increased at 3 HPI. Expression of both genes then returned to near pre-inoculation levels and remained constant as necrosis later appeared due to a non-host hypersensitive response (HR). Virus-induced gene silencing of NbCYP1 and NbCYP2 resulted in increased susceptibility of N. benthamiana to C. destructivum but did not affect the HR necrosis or population levels of P. syringae pv. tomato. These two cysteine proteinase genes do not appear to be involved in the programmed cell death of the HR resistance to P. syringae pv. tomato, but they are involved in limiting the host's susceptibility to C. destructivum.