There have been only limited studies on the effects of harmful algal blooms (HABs) on natural rocky intertidal ecosystems. From mid-September to early November 2021, an unprecedented HAB hit the Pacific coast of southeast Hokkaido, Japan, for the first time causing massive mortalities among marine organisms. To determine how the HAB affected the population sizes of four functional groups—macroalgae, sessile invertebrates, molluscan grazers, and molluscan carnivores—at regional and local scales, census data for 17 years before the HAB and within one month following the HAB for five shores on the southeast coast of Hokkaido were compared. Although the population sizes of three functional groups (macroalgae, sessile invertebrates, and molluscan carnivores) were not significantly different, the population sizes of three species of molluscan grazer were reduced at regional and local (one shore) scales. This suggests that the impacts of the HAB in southeast Hokkaido on population sizes of rocky intertidal organisms are highly variable depending on species and locality, presumably because of differences in species-specific tolerances to HAB toxins and spatial variation in the density of the HAB organisms.