Wildflower viewing is recommended as a form of ecotourism in protected areas to facilitate conservation practices; but this relationship between the conservation of attractive flowering plant species and whole plant diversity has not been quantitatively evaluated. The Kirigamine Plateau in Japan encompasses a protected area that supports high grassland species diversity. Browsing activity by the expanding sika deer populations has negatively impacted this region in recent decades, drastically decreasing blooming flower resources that attract ecotourism. The effectiveness of conserving plant diversity through the placement of deer fences by local conservation practices was evaluated, and indicator species requiring future conservation strategies were identified. Compared to outside the deer fences, the five species diversity metrics (flowering plant richness, flowering abundance, flowering functional diversity (flowering FD), plant species richness, and threatened plant species richness) were significantly higher inside the fences. Except for flowering FD, plant species richness was positively correlated with all other species diversity metrics. The important species analysis identified four species as indicators of conservation for plant diversity and flowering FD out of the top 20 indicator species. The construction of deer fences had a strong positive effect on the preservation of four diversity metrics. However, to conserve flowering FD, additional strategies need to be implemented in this area. Conservation planning based on flowering plant diversity and cultural ecosystem services is vital in reducing the loss of biodiversity in semi-natural grasslands in protected areas worldwide.