Rice (Oryza sativa L.) is the most important staple food for half of the world population, particularly for the people in Japan, Korea, China and the southeast Asia with rice as the daily diets. Rice research progressed greatly in the past years, highlighted by the completion of the first high-quality rice genome in 2005, that stimulated global efforts in rice functional genomics research. Because of the important states of rice in the food security, improving the yield of rice is the most important work during the last several decades. So far, the yield of rice still is one of the important traits for breeders and researchers. However, the eating quality of rice will be one of the most important research areas, with the further development of social economy and living standard. The fragrance in rice is one of the most important sensory qualities. Rice grains with a fragrance are appealing to consumers, and the retail price of fragrant rice is higher than that of conventional rice. Thus, fragrance is an important trait for many breeding programs.BADH1 and BADH2 are two homology genes, encoding betaine aldehyde dehydrogenase in rice. In previous studies, non-functional BADH2 was widely proved as the key factor in determining fragrance in rice, while BADH1 was considered to be a contributor to abiotic stress tolerance. However, recent studies found that BADH1 and BADH2 were proposed to have overlapping functions. In this study, we used 295 rice cultivars and 10 wild rice accessions to determine the polymorphisms and functions of those two genes. Twenty-five SNPs and InDels were detected in transcription region. Association study showed BADH1 has significant correlation with salt tolerance in rice during germination stage, while BADH2 was only responsible for fragrance. According to linkages disequilibrium, nucleotide diversity, Tajima’s D and extended haplotype homozygosity analysis of 4-Mb flanking region of each BADH genes, BADH2 was identified as an important gene contributing to the domestication of rice, while BADH1 was not.