Differences in life-history strategy are thought to contribute to adaptation to specific environmental conditions. Among life-history traits in plants, flowering time and shoot morphology are particularly important for reproductive success. Even though flowering time and shoot morphology are linked, the evolutionary changes in the genetic circuitry that simultaneously affects both traits remain obscure. Here, we have identified changes in a putative pre-mRNA processing factor, HUA2, as being responsible for the distinct shoot morphology and flowering behavior in Sy-0, a natural strain of Arabidopsis. HUA2 has previously been shown to positively regulate two MADS box genes affecting flowering time (FLOWERING LOCUS C [FLC]) and floral patterning (AGAMOUS [AG]) [1, 2]. We demonstrate that natural changes in HUA2 activity have opposite effects on its known functions, thus having implications for the coordinate control of induction and maintenance of floral fate. The changes in Sy-0 lead to enhanced FLC expression, resulting in an enlarged basal rosette and aerial rosettes, whereas suppression of AG function favors a reversion of floral meristems from determinate to indeterminate development. Natural variation in HUA2 activity thus coordinates changes in two important life-history traits, flowering time and shoot morphology.