Submergence stress has severe harm to rice (Oryza sativa L.) production. It is important to identify molecular markers associated with tolerance to submergence for marker-assisted selection (MAS). F1 and F2 populations ware obtained from reciprocal crosses between submergence tolerant parent FR13A and submergence sensitive parent IR39595-503-2-1-2. No difference in reciprocal crosses in F1 population was detected for tolerance to submergence. This indicates that the submergence character is controlled by nucleic factor(s). Tolerance to submergence derived from FR13A appeared to be a quantitative-qualitative trait as revealed by the segregation of F2 population in two submergent experiments. Under light submergence stress, multiple minor genes might work and the trait inherited quantitatively it appeared a quantity trait, While under severe submergence stress, it exhibited a qualitative inheritance controlled by a major gene. Among the 187 pairs of SSR primers, 73 (39%) were polymorphic between the two parents and were used to tag submergence in the F2 population. Primer RM219 was detected to be linked to submergence tolerant trait loci. This result confirmed that tolerance to submergence is controlled by the major gene sub1, which will be helpful in improvement of the trait in rice.