Drought is a major constraint affecting rice production, especially in rainfed areas of mountainous regions of Vietnam. Development of drought tolerant varieties will improve rainfed rice production. Identification of drought-tolerance of the lines and local cultivars is useful for the development of genetic material and rice breeding for adaptation to rainless environments. Forty two rice accessions were evaluated for germination and seedling characteristics by treatment of rice seed with KClO3. The plants were planted In PVC pipe to evaluate root length and root growth under well-watered and water-stressed environments. In addition, OTLs associated with root lengthen and root growth were analyzed using SSR markers. The authors have identified 11 accessiopns (lines and local cultivars) with drought tolerance. Three best drought tolerant accessions, 455 (Khau Ii on/Q5), 464 (Mua chua, Dien Bien) and 487 (Khau Lech, Bac Kan) are recommended for rice breeding program for rainfed environment.