Screening for submergence tolerance and aroma in selected rice varieties of Tripura and their segregants were done both phenotypically and using linked molecular markers. Allelic specific amplification using primers derived from putative BAD2 gene for aroma could identify parents and two heterozygous lines derived from Basmati 370 x Pyzum and three homozygous aromatic lines from Pyzum x Binni cross. SSR marker, RM219 linked to Sub-1, could identify one submergence tolerant line derived from Basmati 370 x Pyzum. Although no aromatic line was found submergence tolerant in the current investigation, but the consistency of this screening process, would help in selecting aromatic lines with submergence tolerance from hybridization program involving traditional varieties of Tripura.