Assemblages of sandy shores are primarily structured by physical environment factors. This structuring provides a unique opportunity to evaluate biogeographic regions. In this study, the shallow subtidal zone (0.2–1.2 m) of 39 sites of sandy shores along the Japan Sea coast of Honshu were surveyed using a sledge net to identify invertebrate assemblages and to elucidate their relationships with environmental factors and geographic distributions. In total, 78 taxonomic units were obtained and six clusters of assemblage were recognized according to the Morisita-Horn dissimilarity index values between the assemblages of these sites. Indicator taxonomic units were identified for the clusters and a distance-based redundancy analysis (dbRDA) demonstrated that a set of five environmental factors (slope angle of the swash zone, sediment grain size, average wave fetch, spring sea surface temperature, and summer Chlorophyll-a concentration) significantly explained variations of the assemblages. Geographical distributions of two of the clusters were localized and mutually exclusive (one in the north and one in the south), while the other four clusters were scattered along the coast. On the dbRDA ordination, these two clusters were plotted on opposite ends of the 1st axis on which spring sea surface temperature and summer Chlorophyll-a concentration showed high contributions. The spatial gap between the two clusters was located in an area between the Noto Peninsula and the Sado Island, central Honshu, which can be proposed as a boundary of geographic regions of sandy shore organisms along the Japan Sea coast.