The fragrance of rice is one of the premium characteristics that breeders want to include in the rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase Isoform 2 (BADH2) are reported to associate with fragrance of the rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica types through the Bayesian phylogenetic approach and haplotype network analysis of the 3K Rice Genome Project. In addition, the report also contributed a new set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identifying the 13 bp deletion only within NTCD (no amplified band) compared to both non-aromatic and aromatic rice varieties (110 bp band). This study also found that the deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon in the mature transcript, which down-regulated expression of the BADH2 transcript while associated with up-regulation of P5CS and the high amount of 2-acetyl-1-pyrroline. This study reported the potential of using a deletion in exon 7 of the BADH2 gene as novel marker for adulteration and breeding of fragrant rice varieties, particularly Nang Thom Cho Dao