Rhizoctonia solani is one of the most destructive pathogens causing foot rot disease on tomato. In this study, the molecular and cellular changes of a partially resistant (Sunny 6066) and a susceptible (Rio Grande) tomato cultivar after infection with necrotrophic soil-borne fungus R. solani were compared. The expression of defense-related genes such as chitinase (LOC544149) and peroxidase (CEVI-1) in infected tomato cultivars was investigated using semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). This method revealed elevated levels of expression for both genes in the partially resistant cultivar compared to the susceptible cultivar. One of the most prominent facets of basal plant defense responses is the formation of physical barriers at sites of attempted fungal penetration. These structures are produced around the sites of potential pathogen ingress to prevent pathogen progress in plant tissues. We investigated formation of lignin, as one of the most important structural barriers affecting plant resistance, using thioglycolic acid assay. A correlation was found between lignification and higher level of resistance in Sunny 6066 compared to Rio Grande cultivar. These findings suggest the involvement of chitinase, peroxidase, and lignin formation in defense responses of tomato plants against R. solani as a destructive pathogen.