Accessions of cucumber were screened under greenhouse conditions for resistance to crown and root rot caused by Phytophthora capsici. Two cucumber accessions were selected, which had significantly lower disease severity compared to the commercial cucumber cultivars evaluated. A real-time PCR protocol was validated to detect and quantify P. capsici in crown and root tissue of cucumber and pepper, there is a positive correlation between P. capsici susceptibility and levels of pathogen colonization in plants. Additionally, the activity of peroxidase (POD), polyphenol oxidase (PPO), and superoxide dismutase (SOD) were analyzed in crown and root tissues of cucumber and pepper after P. capsici with the pathogen. POD activity appeared to be related to P. capsici resistance in pepper. None of these enzymes were related in cucumber P. capsici resistance. The results of this study provide valuable information for developing effective disease management approaches in breeding programs.