The soilborne necrotrophic fungal pathogen Macrophomina phaseolina (Tassi) Goid causes charcoal rot disease in many economically important crops. There are no effective control methods for this disease and no completely disease-resistant cultivar has been identified in crop species against M. phaseolina, including alfalfa, soybean and sorghum. In our previous study, we have established a pathosystem using the model legume Medicago truncatula to study the molecular interactions between the pathogen and its host. In this study, we investigated the possible variability in host response to M. phaseolina infection among different Medicago ecotypes. We found that disease progression in different ecotypes had little variation, and no ecotype was identified that showed resistance. We have previously found that methyl jasmonate (MJ) and ethylene (ET) could induce partial resistance in Medicago ecotype A17 against M. phaseolina. Here, we compared the disease progression after MJ or ET! treatment between A17 and R108, another commonly used ecotype. Unlike A17, our results showed that R108 plants treated with MJ and ET did not show any induced resistance to M. phaseolina. The possible molecular mechanisms that led to these variations are further discussed.