Great losses to cucurbits and peppers in greenhouses are caused by Oomycetes fungus like organisms annually. To determine the causal agent and the extent of damage caused by disease, several greenhouses in Isfahan and Yazd provinces were surveyed during this research. Phytophthora root rot and Pythium damping-off were observed in all greenhouses and average disease was recorded from 5 to 75 percent. Diseased samples were collected and sixty Phytophthora and Pythium specimens were isolated on different media. Based on morphological and limited physiological characteristics, 40 isolates were identified as Phytophthora melonis , 10 as P. capsici and 10 isolates as Pythium aphanidermatum . Pathogenicity tests were conducted using all isolates and results revealed that all isolates were pathogenic on cucumber and bell pepper. To distinguish P. melonis and P. drechsleri from each other, potato pink rot and safflower root rot tests were carried out, that was shown same result. Genomic DNA was extracted using Silva et al. method and different regions of genomic DNA e.g. ITS, Tef and B-tubulin genes were amplified by three sets of primers: ITS 1 /ITS 4 , Tef 1 /Tef 2 and bt 1 /bt 2 . Two sets of species - specific primers CAPFW/CAPFRV 1 and CAPFW/CAPRV 2 were used to identify P. capsici , also two sets of species - specific primers Pa 1 /ITS 2 and Pa 3 /ITS 2 were used to identify Pythium aphanidermatum. PCR-RFLP of ITS region using Rsa I, Hin fI, Taq I, Hpa II and Hae III restriction enzymes was carried out. PCR-RFLP method, potato pink rot and safflower damping-off tests couldn ’ t distinguish P. melonis and P. drechsleri from each other, so it is necessary to design species - specific primers to provide informative results.
