The evaluation of genetic diversity is important for the conservation of species. However, changes in genetic diversity during conservation are complex processes that depend on the characteristics of the species and environment. To evaluate the changes in genetic diversity from decline to recovery, we surveyed the coastal herb Calystegia soldanella in areas with varying degrees of non‐coastal plant invasion. First, to evaluate genetic diversity before the conservation measures, the spatial clonal structure of adults was investigated in a population invaded by non‐coastal plants. Second, to evaluate genetic diversity after the conservation measures, the regenerated individuals were investigated in the restoration plot. Moreover, to predict future genetic diversity without conservation measures, the effects of non‐coastal plant invasion on the production and genetic diversity of seeds were investigated using individuals from areas with various levels of non‐coastal plant invasion. In the adult population, 16 genets were identified in an 80 m × 4 m area. The maximum genet size was 30.3 m, suggesting the importance of clonal reproduction for population maintenance. In the restoration plots comprising 10 m × 10 m × 3 replicates, many seedlings (1.14 ramets/m2) emerged, resulting in high clonal diversity compared to that of the adult population. Therefore, the biomass and genetic diversity were rapidly restored at the beginning of the conservation practice. Non‐coastal plant invasion did not affect the genetic diversity of the seeds. However, it significantly reduced seed production. This suggests that non‐coastal plant invasion reduces sexual reproduction, resulting in the long‐term loss of genetic diversity.