Rice cultivation by direct seeding allows reduced labour and production costs in addition to other benefits. However the success of this rice production method can be limited by uneven fields with poor drainage or heavy rainfall at sowing leading to early flooding conditions slowing germination and hindering crop establishment. Hence, the need to improve tolerance to anaerobic conditions in both rainfed and irrigated rice ecosystem after direct seeding. In this study QTL analysis was performed to identify QTLs associated with tolerance derived from Vietnamese variety Tai Nguyen (TN) under anaerobic conditions during germination. The population derived from a cross between TN (tolerance indica lines) and Anda (susceptible japonica), was used for collection of phenotypic data based on the survival rates of the seedlings at 21 days after sowing under 10cm of water. A total of 286 F2:3 families of the population were used for QTL mapping and the genotyping was carried out with the infinium 6K SNP-chip based on the illumina infinium platform. Two significant QTLs associated with the AG trait were detected on chromosomes 1 and 11, respectively. In Particular, the QTL on chromsome 1 had an LOD score of 7.45 and R2 of 14.21%. We plan to confirm the identified QTLs in further studies and develop varieties with improved anaerobic germination ability using advanced backcross lines.