Phytophthora melonis is the causal agent of damping-off or crown rot, one of the most destructive cucumber disease that causes severe economic losses in in Iran and some other parts of the world. Despite intense research efforts made in the past years, no permanent cure currently exists for this disease. With the aim to understand the molecular mechanisms of defense against P. melonis, root collars and leaves of four cucumber genotypes consisting of resistant Ramezz; moderately resistant Baby and very susceptible Mini 6-23 and Extrem, were monitored for quantitative gene expression analysis of five antifungal and/or anti-oomycete genes (CsWRKY20, CsLecRK6.1, PR3, PR1-1a and LOX1) at three points after inoculation with P. melonis. The gene expression analysis indicated that P. melonis strongly enhanced the expression of these genes after inoculation in both leaves and root collars. Further, not only the transcript levels of these genes were significantly higher in the resistant and moderately resistance genotypes, but also the time point of the highest relative expression ratio for the five genes was different in the four cucumber genotypes. CsWRKY20 and PR3 showed the maximum expression in Ramezz at 48 hpi while CsLecRK6.1, and LOX1 showed the highest expression at 72 hpi. In addition, PR1-1a showed the maximum expression in the Baby at 72 hpi. Root collars responded faster than leaves and some responses were more strongly upregulated in root collars than in leaves. The genes found to be involved in disease resistance in two different organs of cucumber after pathogen infection. The results suggest that increased expression of these genes led to activation of defence pathways and could be responsible for a reduced P. melonis colonization capacity in Ramezz and Baby. Overally, this work represents a valuable resource for future functional genomics studies to unravel the molecular mechanisms of C. sativus- P. melonis interaction.