In this study, an association analysis of pepper (Capsicum annuum Linnaeus) resistance to Phytophthora capsici Leonian was performed in a pepper core collection of 194 C. annuum Linnaeus materials. By taking use of 58 pair of SSR markers, 178 allelic variations were detected. The average shannon index, polymorphism information content (PIC) and gene diversity were 0.6732, 0.3859 and 0.4400, respectively, implying a high level of polymorphism within the diversity panel. The structure analysis suggested two sub-populations, correlating with the difference on levels of resistance. Twelve of 58 SSR loci were found to be associated with disease index, with an explanation of 2.98%-16.05% of the phenotypic variance. Fifteen SSR loci were identified to be associated with diseased plant rate, which could explain 2.95%-21.29% of the phenotypic variance. The locus explaining the largest phenotypic variance was assigned to chromosome 7, and the other loci with minor effects were found on chromosome 2, 3, 7, 8, 9 and 11. Furthermore, which indicates the materials in this study probably contain novel P. capsici Leonian resistant alleles. The alleles with the largest minor effects in each associated locus were elite alleles for P. capsici Leonian resistance, including CM0005c, ge35-141pmH0135Cd, Hpms1-139c, etc. Based on these elite alleles, a series of excellent carrier materials were explored, including germplasm 171, 55, 161, 65, 132, 128, 91, 106, 125, 127, 169, etc. Taken together, the resistant alleles and carrier materials explored in this study provided valuable natural resources in marker-assisted selection breeding for P. capsici Leonian resistance varieties in the future.