Pepper, Capsicum annuum is one of the most important crop products in the world, which has grown widely and significantly in the greenhouses, due to the importance of its food and its significant consumption during last several years in the country. Different diseases threaten the growth and development of pepper product. But, currently, a fungal disease, Phytophthora capsici is with high severity on peppers. Pepper root and crown rot, Ph. capsici is one of the important diseases in Iran and around the world. In this study, the phenology morphology and pathogenicity of pepper root and crown rot disease isolate were analyzed. These isolates were obtained from various region including, Marvdasht, Dehaghan, Shiraz, Shoosh, Ramhormoz, Shahrood, Shahreza and Ghazvin. Thus, the studied at laboratory, with the isolates, from a distinct regions and or different provinces, were carried out on various culture media, and the dry and fresh mycelium weights and sporangium variation were determined accordingly. Variance on mortality rate of pepper plants at different stages of development for varieties was analyzed by SAS software separately and in combined at 1% probability level, and the means with using Duncan's multiple range test, DMRT and T test, and cluster analysis was performed by drawing a dendrogram and genotyping by software (SPSS, SAS). The results at laboratory levels indicated, that the isolates reacted differentially and significantly on the various measured parameters including, different culture media, PDA and CMA where, the maximum was of Shahreza and Ghazvin, the lowest and also, the fresh and dry mycelium weights on liquid media indicating the maximum in Ghazvin and the least in shoosh isolates, and the rest were in between. The morphology of sporangia indicated variability in length, papilla and shapes too, which Ramhormoz, was the highest and Shahrood the lowest whereas, in the case of papilla, Shoosh was the highest and Shahrood the lowest and the rest in between. Also, these examined isolates were assessed against each other for the disease development and severity determination in glasshouse conditions on pepper plants grown in pods containing sterile soil. The results indicated that, they were also varied in pathogenicity tests and statistical analysis, SAS, divided the isolates to various distinct groups. Showing a great variation in between the examined peppers plants with a great and significant affects where, the cluster analysis also, divided the above isolate into distinctive groups too in order to confirm the SAS results as far as the variability in phenology, morphology and pathogenesity in the form of growth parameters such as percent mortality, length, dry and fresh weights of the root and shoots are concerned.