Plants have the ability to generate new leaves continuously throughout their entire lifespan due to the persistent activity of stem cells in their vegetative meristems. During the reproductive phase, the floral meristem (FM) produces all floral organ primordia in sequential whorls or spirals. Unlike the vegetative meristem, the stem cell activity of FMs will always terminate at a specific time point during primordia initiation, since each flower only has a finite number of organs. Variation in the timing of FM termination (FMT) is an essential source of generating floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is still poorly understood. Aquilegia is a well-suited system for investigating this fundamental process, since flowers from different Aquilegia species have identical numbers of all floral organs except for stamens. Therefore, the variation in the timing of FMT can be represented by the variation of stamen whorl numbers in the flowers. We generated a F2 population by crossing A. canadensis and A. brevistyla, which are sister species with mean stamen whorl numbers of 9.15 and 7.16 per flower, respectively, and performed quantitative trait loci (QTL) mapping. We have phenotyped 4265 flowers for their stamen whorl numbers and conducted whole genome sequencing in 364 F2 individuals. Initial mapping revealed five major QTLs that are responsible for an estimate of 48% variation in stamen whorl numbers. Fine-mapping is currently in progress and we will be conducting functional studies of promising candidate genes. This is the first study to investigate the nature of variation in the timing of FMT, and our results will provide critical insight into how floral morphological diversity is generated at the meristematic level.