Farmers in developing countries rarely know true variety names of crops they grow. In this paper, we identify rice variety identity with DNA fingerprinting by using an advanced gynotyping technique of 1,302 rice seed samples collected from total of 544 farmers in Bangladesh in 2014 and 2015. To identify farmers’ varieties, we compare the DNA information of farmers’ seeds against three DNA data sources: Bangladesh breeder seeds, Indian breeder seeds, and IRRI gene resources which include previously collected improved and traditional rice varieties. In particular, our analysis includes identification of submergence-tolerant rice varieties which have been developed and distributed in Bangladesh in recent years. The results indicate that about 7% of the seed samples were identified as submergence-tolerant rice varieties, i.e., BR11-Sub1 (5%) and Swarna-Sub1 (2%). Other modern varieties were also identified by DNA fingerprinting. Farmers’ identification of varieties was found poor, especially on old varieties. Simple adoption models indicate that the estimation results are unreliable when farmers’ ability to identify varieties is poor.