Background: Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo ¿Piel de sapo¿ (¿PS¿) and C. melo ¿Pat 81¿, with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. Results: Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. ¿PS¿ responded with a more rapid infection response than ¿Pat 81¿ at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in ¿PS¿ declined from 451 to 359, while the total number of differentially expressed transcripts in ¿Pat 81¿ increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in ¿Pat 81¿ compared to ¿PS¿ suggested that JA response might be partially responsible for their observed differences in resistance. Conclusions: As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation. ; Roig Montaner, MC.; Fita, A.; Nuez Viñals, F.; Picó Sirvent, MB.; Rios, G.; Hammond, JP. (2012). Root transcriptional responses of two melongenotypes with contrasting resistance toMonosporascus cannonballus (Pollack et Uecker)infection. BMC GENOMICS. 13(601):1-12. doi:10.1186/1471-2164-13-601. ; Senia ; 1 ; 12 ; 13 ; 601