Cucurbits species are economically important crops grown worldwide. In many regions, the most serious threat to their production is Zucchini yellow mosaic virus (ZYMV). A monogenetic source of resistance to ZYMV was identified in Cucurbita moschata and introgressed in a Cucurbita pepo. However, in cultivated zucchini the major dominant gene indicated as Zym-1 interact with other genes, making difficult the breeding transfer. Until now, not effective markers associated to ZYMV resistance have been found in C. pepo. Main goal of this work was to investigate the mode of inherence of ZYMV resistance in zucchini and to identify molecular markers associated with resistance genes to ZYMV, in order to make easier, faster and economically sustainable the introgression of this resistance in zucchini local varieties 'San Pasquale'. Moreover, a genome-wide transcriptional analysis of a resistant and a susceptible genotype to ZYMV was conducted to identify new candidate genes for resistance to ZYMV and to catalogue SNP polymorphic markers. Two F2 and three BC1 segregating populations, obtained from the cross of '381e' (resistant variety) with 'True French' and 'San Pasquale' (susceptible varieties) were assayed for ZYMV resistance. Phenotypic analysis highlighted a complex inheritance of resistance with the involvement at least of three genes (Zym-1, Zym-2 and Zym-3). Molecular segregation analysis conducted using High Resolution Melt (HRM) technology on 3 SNP loci strongly suggested a relationship between these SNPs and resistance genes Zym-1, Zym-2 and Zym-3. Nearly 3000 differentially expressed genes between 'True French' and '381e' isogenic lines for resistance to ZYMV were identified in the transcriptome of susceptible and resistant varieties inoculated with the virus. A high number of SNPs between the two varieties were also evidenced. A close co-localization of SNP1 with a CNL and an ATP-dependent RNA helicase, suggests that one of those genes could be a good candidate for exerting resistance function to ZYMV. The study of ZYMV resistance response in zucchini at genetic and genomic level, performed in this work, can be useful for the genetic improvement of local varieties (as the susceptible 'San Pasquale') that have a good marketability in Campania region.