To reveal the community structuring mechanism of the pebble interstitial macrofauna, we examined the community structure and its relationship with abiotic environmental factors on a pebble beach in Honshu, central Japan (northwest Pacific). Throughout the year-round survey, we found 66 species from 18 classes in 9 phyla, most of which were either endemic or undescribed species. This is a noticeably higher species diversity compared to the common theory (quite low biodiversity) for pebble beaches and also indicates independence from other environments. Moreover, the communities were divided into five groups through clustering, which were significantly explained by sediment particle size and tidal level using RDA (Redundancy Analysis). However, their interpretabilities were moderate, suggesting that the community structure was moderately controlled by environmental factors. This could be owing to the optimization of the benefit of interspecific ecological niche isolation and the cost of recovering from the disturbance. Consequently, the present study reveals the presence of diverse and unique macrobenthic communities that inhabit the pebble beach environment in Japan and are controlled by the abiotic environmental characteristics of microhabitats.