1. The often patchy distribution of serpentine geology can lead to abrupt changes in soil and microclimates. Thus, serpentine areas provide an ideal natural laboratory to understand how divergent selection drives the process of local adaptation in edaphically endemic plant species. In case where the serpentine ecotype is surrounded by related non-soil specialists, a balance of natural selection and potential gene flow should be a key factor to maintain the different ecotypes over very short distances. We aimed to reveal the mechanisms to enable soil ecotypes of a goldenrod species to occur almost sympatric situations in Japan. 2. We performed field surveys to characterize microenvironments and reproductive timings of each ecotype, common garden and reciprocal transplant experiments, artificial crossing, and population genetic analysis. 3. Growth chamber experiments show that serpentine plants showed higher leaf mass per area and greater resource allocation to their root systems than did their non-serpentine counterparts, a potential adaptation to drier soil condition in serpentine habitats. Reciprocal transplants demonstrated a clear pattern of local adaptation in the plant growth rate. Importantly, serpentine populations completed flowering by mid-summer versus late summer in non-serpentine plants. This pattern is consistent with the hypothesis that early flowering ensures reproductive success, before the microclimatic conditions becomes severest in open habitats. Although prezygotic isolation was a strong barrier to gene flow, genetic differentiation was very low, indicating a recent origin for the serpentine ecotypes and/or gene flow at low frequencies. 4. Synthesis. The findings indicate that the early-flowering times of serpentine ecotypes, which would have been selected for by microclimates in serpentine areas, can play roles in local adaptation, but also population isolation via a by-product of diverged reproductive timings. This study contributes to general understanding of the initial stages of plant ecological speciation under potential gene flow in very small geographic scales.