A study was conducted during rabi 2008–09 to validate eight simple sequence repeat (SSR) markers for fertility restoration ability of 97 drought tolerant advanced breeding lines of rice (Oryza sativa L.) with one wild abortive (WA) based cytoplasmic male sterility (CMS) line in their 97 F1S. The spikelet fertility percentage (SF%) was taken as criteria for restoration ability of lines, based on this IR 83641-518-B, IR 79915-B-83-4-4 and IR 80508-B-57-2-B were considered as the best restorer lines for WA based CMS line and used further for validation of SSR markers. Out of eight, only four markers, namely, RM 7446, RM 6100, RM 25661 and RM 25662 produced significant polymorphism between restorer and male sterile parents, were validated as they linked tightly with fertility restore (Rf) genes. These markers may facilitate marker assisted selection (MAS) of restorer lines in CMS-WA system from large source nurseries to avoid routine testcrosses in hybrid rice breeding programmes.