Uncultivated periods are important in rice paddy fields for the survival of species favoring unaerated soils. Clarifying the mechanisms affecting the floristic diversity of in-field habitats is a key part of sustainable agriculture. We hypothesized that the timing of crop harvest influences the flora in the subsequent uncultivated period in rice paddy fields. To confirm this hypothesis, surface soils were sampled in cultivated paddy fields at the beginning of August.The sampled soils stored in ≤ 5% relative light intensity were exposed to direct light at different periods varied from late August to the beginning of October. Germinated seedlings were counted until spring the next year. Observation in autumn showed that the numbers of species, germinated individuals, and flowering individuals differed as a function of the duration of light exposure, although these differences were less clear in the subsequent spring. These differences can be explained by differences in ecological traits such as maturation rate and optimum germination temperature. Timing of the rice harvest is closely linked to the timing of rice planting, which in turn can affect the germination of species maturing before the rice is planted.