Coastal sand dune ecosystems have been lost and increasingly fragmented due to human use and disaster prevention over the past few decades. Generally, habitat fragmentation and connectivity loss have led to the decline of species biodiversity. In coastal dune ecosystems, habitat loss across the coastal gradient may be a major driver of the decline in coastal species diversity and ecosystem functions. In this study, we assessed the species richness of coastal plants and hymenopteran insects in fragmented coastal dunes of Japan using six sites with and without back-dune habitats. We recorded plant species and their flowering status monthly from April to September 2018 and examined the effects of landscape factors on plant species richness. We also assessed the species richness of hymenopteran bees and wasps and compared their determinants with those of plants. In total, we identified 109 plant species, including 33 native coastal plants (10 of which are endangered) and 40 exotic plants. The number of native plant species was positively affected by the presence of back-dune habitat and sand dune size, while that of native coastal plant species was positively affected only by the presence of back-dune habitat. In contrast, the number of exotic plant species was dependent only on sand dune size. We recorded 58 hymenopteran species including 28 bee pollinators and 30 predatory wasp species. The number of hymenopteran species was positively related to the number of native plant species for both bees and wasps. In conclusion, habitat loss across the coastal gradients led to decreased species richness of native coastal plant species, resulting in reduced species richness of pollinator and predatory insect communities. Most of the coastal areas across sea-to-inland gradients have been lost due to recent disaster prevention activities. Our results highlight the urgent need for biodiversity conservation of endangered species in remnant coastal dune ecosystems.