Pepper (Capsicum sp.) with numerous variations having abundant utilizations such as ornamental, food and pharmaceutical aspects. In this research, the genetic diversity of 37 resistant and susceptible ornamental and edible pepper genotypes to damping-off disease, caused by Phytophthora capsici, was analyzed by 47 morphological attributes and 20 ISSR primers. Results of ISSR assay indicated that 19 primers out of 20 primers produced scorable polymorphic bands. Totally, 188 bands were produced, which 185 bands were polymorphic. The polymorphism mean percent (P%) in ISSR markers was 98.5% and on average, 9.9 bands were produced using each primer. Polymorphism percent varied from 78% to 100%. Average of polymorphism information content (PIC) was 0.449. Based on the results of ISSR analysis, the genotypes were divided into five main groups. Morphological attributes also divided the genotypes into five distinct groups. Correlation between molecular and morphological similarity coefficients was non-significant. The screening results of resistance to damping-off disease demonstrated that five genotypes including 11BlockyP-YToran, 19OrnP-PBI, 23CherryP-Orsh, 32OrnP-China and 37ChilP-Paleo, which have the lowest mortality at seedling and maturity stages, were belong to ornamental and long peppers groups. The correlation coefficient of genetic diversity and resistant of the related genotypes to damping-off, Phytophthora capsici clustered the five resistant genotypes except 37ChilP-Paleo in one morphological group and all five genotypes were placed in four different molecular groups.