In Yakushima Island, 82 plant species are reported to be miniaturized, mainly in the alpine area. Among these alpine dwarf plants, dwarfed Lysimachia japonica has been well examined morphologically and genetically by comparative studies with the lowland normal-sized L. japonica. Our previous study showed that leaves are especially smaller at the organ level in the dwarfed L. japonica, and the smaller leaf has both a smaller number of cells and a smaller cell size. In the present study, we examined whether the dwarf morphologies are genetically controlled or not. And also, if these dwarf morphologies are genetically controlled, we examined whether these dwarf morphologies are adaptive traits or not. To answer these questions, a common garden experiment and population genetic analysis were performed. The results of the common garden experiment revealed that the plants from the highland were significantly smaller in nine traits mostly associated with plant size, suggesting that the dwarf morphologies of L. japonica are genetically controlled. Every Qst value of the morphological characters measured in the common garden experiment was significantly higher than the Fst value (0.24) calculated using neutral genetic markers, suggesting that the dwarf morphologies of L. japonica that occur in the alpine region in Yakushima have been evolved as adaptive traits.