In lotic wetlands, runner reed (Phragmites japonicus) plays a role as a pioneer, which helps other plant species to settle by making dense roots trapping floating-sediments. In lentic wetlands, on the other hand, P. japonicuscould play a role as an invader threatening biodiversity by forming tall and dense stands. To conserve an abandoned paddy terrace in mountainous areas, a habitat of an endangered dragonfly species (Nannophya pygmaea), from the monotypic-occupation by P. japonicus, we applied three kinds of treatment: (1) hand-clipping in 2009, (2) mechanical excavating in 2012, and (3) planting of alternative vegetational unit in 2012. We have monitored vegetation changes in the wetland in 2008~2012 and 2017. Vegetation cover of P. japonicussharply decreased from 43% in 2011 to 16% in 2012 by the mechanical excavation. After 5 years from applying the treatment, Schoenoplectiella mucronatathat was utilized in the planting became the predominant species instead of P. japonicusand the number of wetland plant species increased from 16 to 25 with the shift in species composition. This study showed the utility of three control methods of P. japonicasin a lentic wetland.