Technical Abstract: Molecular markers closely linked to genes that confer a high level of resistance to root-knot nematode (RKN) in the germplasm derived from Auburn 623 RNR would greatly facilitate cotton breeding programs. Our objectives were to identify SSR markers linked to RKN resistance QTLs and map these markers to specific chromosomes. We developed three recombinant inbred line (RIL) populations by single seed descent from the crosses of RKN resistant parents M-240 RNR (M240), developed from the Auburn 623 RNR source, moderately resistant Clevewilt 6 (CLW6), one of the parents of Auburn 623 RNR, and susceptible parent Stoneville 213 (ST213). These crosses were CLW6 x ST213, M240 x CLW6, and M240 x ST213. RILs from these populations were grown under greenhouse conditions, inoculated with RKN eggs, and scored for gall index and number of eggs per plant. Plants were also genotyped with SSR markers. Results indicated that a minimum of two major genes were involved in the RKN resistance of M240. One gene was localized to chromosome 11 and linked to the marker CIR 316-201. This CIR 316-201 allele was also present in CLW6 but not in Mexico Wild (MW) (PI593649), both of which are parents of Auburn 623. A second RKN resistance gene was localized to chromosome 14sh and was linked to the SSR markers BNL 3545-118 and BNL 3661-185. These two marker alleles were not present in CLW6 but were present in MW. The SSRs identified in this study should be useful to select plants with high levels of RKN resistance in segregating populations.