A mapping population comprising 220 F2 individuals was developed by raising the selfed F1 seed of a single hybrid plant, White Ponni x Moroberekan. Two hundred and twenty two F3 families were phenotyped for blast resistance under artificial condition. Fifty random amplified polymorphic (RAPD) primers were used to identify parental polymorphism. Twelve RAPD markers which showed clear polymorphism were scored in the F2 mapping population. Out of 12 markers, 11 loci (91.97 %) fitted into the expected segregation ratio of 3:1 based on χ2 - test at 0.05% probability value. Four hundred microsatellite primer pairs were used in the parental survey, Out of which 52 simple sequence repeats (SSR) primers were polymorphic. Out of 52 marker loci, 44 marker loci (84.61%) fitted into the expected Mendelian segregation ratio of 1:2:1 based on χ2 - test at 0.05% probability value. The multipoint analysis resulted in the construction of preliminary genetic linkage map with 40 loci. One way analysis of variance (ANOVA) was performed to identify the marker phenotype association which resulted in the identification of 23 SSR markers putatively associated for the six traits studied. Three SSR markers (RM 5757, RM 451 and RM 492 from chromosomes four and two) were linked for leaf blast resistance, six markers for days to flowering, nine markers for pigmentation trait, two markers for plant height, four markers for panicle length and seven markers linked for grain yield per plant. Out of 12 RAPD markers studied, 7 were found to be linked to three traits viz., leaf blast resistance (OPBB 5258, OPBB 5194, OPAL 16940 and OPBD 12680), five markers for glume purple tip (GPT) and one marker for grain yield per plant based on single marker analysis. © 2011 Academic Journals.