The entire spectrum of cultivated turmeric germplasm available today is highly susceptible to rhizome rot disease caused by necrotrophic oomycete Pythium aphanidermatum. Conventional host resistance breeding approaches have not been very successful in the crop owing to its lack of genetic variability, obligatory asexual nature and stigmatic incompatibility. The present study sought to develop easy, rapid and reliable molecular markers to identify new turmeric germplasm that could be used as source of resistance to P. aphanidermatum. Bulk segregant analyses using pooled DNA from resistant and susceptible genotypes with 40 inter simple sequence markers resulted in the isolation of a putative resistance specific marker ClRSM. The resistance specific fragment was converted into a sequence tagged marker ClSTS, which could successfully amplify a 720 bp, fragment in resistance turmeric genotypes but not in the susceptible plants. Southern blotting confirmed it as a single copy locus found associated with the resistant genotypes. Further, the ClSTS marker precisely identified 10 resistant and five susceptible genotypes among the 15 turmeric germplasm with unknown disease response collected from different agroclimatic regions. Inoculation assessment of the 15 individuals with a virulent strain of P. aphanidermatum corroborated with the STS marker results. Hence, the identified STS marker can be use as an efficient tool for early and rapid identification of new turmeric cultivars resistant to rhizome rot through marker-assisted selection.