<p>Flavonoids are key therapeutic compounds in rice. This study aimed to develop genetic stocks with high flavonoid content by analyzing 235 F₅ rice lines derived from ADT48 (low flavonoid) x Kavuni (high flavonoid). The morphological, molecular and biochemical analysis of the F₅ population revealed that the main flavonoid content in the donor parent was quercetin and respective genomic regions could be transferred to the high-yielding, low flavonoid parent background through recombination breeding. Further, a positive correlation was found between total flavonoid content and panicle length and hundred-seed weight, indicating the potential for simultaneous improvement of yield and flavonoid content. The SSR markers RM228 and RM5348 had R² values of 0.5439 and 0.1619, respectively. RM228 was found to have a high R² and strong linkage with the candidate gene flavonol synthase and hence could be considered as the reliable SSR marker for selecting high flavonoid content progenies in early segregating generations. Three F₅ recombinants were found to have elevated TFC with the appreciable performance of yield-related traits along with medium slender grains. This indicates that flavonoid content in rice can be enhanced through recombination breeding, without adversely affecting yield or grain quality.</p>