Drought and submergence are the two major limiting factors that reduce rice production. In this study, the relevance of yield traits through path analysis under drought and submergence conditions to improve grain yield of rice, from dry season 2014-2015 and genotypic analysis using SSR markers was evaluated, during 2015-2016. Path analysis indicated that the number of panicles/clusters had the highest and a direct positive effect on the grain yield, followed by the number of filled-grain/panicle, and the harvest index compared to other component traits. These traits could be used as selection criteria for high yield and drought tolerance in populations of rice. There were two markers including RM201 (210-225 bp) and RM219 (210-215 bp) chosen to select parents in backcrossing because production of polymorphic bands relevant to submergence and drought tolerance genes. By the BC1F1 and BC2F1 generations of the cross OM6162/Swarnasub1//OM6162, primers RM201 and RM219 were identified drought and submergence tolerant individuals. These lines will be used in breeding programme for release of both drought and submergence tolerant with considerable yield in next step. Findings of this study are promising to develop rice cultivars tolerant to both drought and submergence, and may therefore help to reduce detrimental impacts from climate changes to rice production.