A segregating doubled haploid (DH) population (n = 96) was developed by anther culture of an F₁ plant crossed between susceptible (‘Manganji’) and resistant (‘Criollo de Morelos 334’) lines of pepper (Capsicum annuum L.) to conduct a genetic analysis of resistance to Phytophthora rot caused by Phytophthora capsici. In order to perform a quantitative trait locus (QTL) analysis, we constructed a high density simple sequence repeat (SSR)-based map with a total length of 878 cM. Sixteen linkage groups (LGs) and 118 SSR markers were located using the 626 SSR markers that we previously developed. Resistance was evaluated in two root inoculation tests. Interval mapping for the resistance to P. capsici detected a common major QTL in the duplicate tests and a minor QTL specific to the first test. The major QTL was located on LG15 and flanked with an SSR marker, CAMS420. In addition, seven SSR markers were located within 21 cM intervals from the peak of this QTL. In contrast, the QTL on LG3 was detected with small effects in the first test, the nearest marker was a dominant amplified fragment length polymorphism (AFLP) marker, and the QTL was surrounded by eight SSR markers within a distance of 10 cM. Since some of the linkage markers for agriculturally valuable traits cannot detect polymorphism within breeding populations in C. annuum, the present linkage markers may widen the choice in marker-assisted selection in breeding programs for Phytophthora rot resistant pepper cultivars.