Rice blast disease is one of the most destructive diseases in rice plant. The short-live of the blast-resistance in rice plant is one of the main constraints in rice production. The easy breakdown of blast resistance for current rice cultivars may be attributed to inadequate techniques and methods in analyzing the pathogen population structure and their evolution, and what we still have not entirely known in the genetic basis of blast resistance in resistant cultivars. In this paper, we review the progress on the application of molecular markers to the analysis of blast pathogen population structure and genetics of blast resistance and on the development of molecular marker techniques in tagging the blast resistance genes. The strategies for sustainable management of blast disease through molecular genetic analysis are discussed. Several problems toward the practical applications in these studies are mentioned at the end of this paper.