Arabidopsis thaliana ecotype Columbia was used as a host in order to investigate the involvement of MAP kinase machinery in the pathogenesis of Alternaria blight. Semi-quantitative reverse transcriptase polymerase chain reaction and quantitative real time PCR based approaches were used to determine the change in transcript profile of MAP2K9 and MAPK6 in leaves of A. thaliana ecotpe Columbia at early, middle and late stages of Alternaria blight infection. It was observed that the expression of both MAP2K9 and MAPK6 simultaneously increased up to middle stage of disease progression. There was observed a positive correlation between the expression of MAPK6 and MAP2K9 as disease progressed from initial to middle stage of infection. Then, the expression of MAP2K9 decreased and that of MAPK6 increased as disease progressed towards late stage of infection. The increased levels of MAP2K9 and MAPK6, seem to be necessary for plant to defend the pathogen up to middle stage of infection. However, MAP2K9 may be down regulated at late stage of infection by pathogen to promote it's efficient colonization. Since MAPK6 expression remains unaltered till late stage, it suggests that it's expression is not only regulated by MAP2K9 but also by other MAP2K's. The above results are consistent with observations of earlier studies. In conclusion, the present study has suggested MAP2K9/MAPK6 module as possible target, which is influenced during pathogenesis of Alternaria blight in A. thaliana ecotype Columbia. Hence genetic modulation in expression levels of these components in Arabidopsis or Brassica could be a possible strategy for engineering defense against Alternaria blight disease.