Global seabird populations are in decline, with nearly half of all seabird species currently in an extinction crisis. Understanding long-term seabird population trends is an essential first step to inform conservation actions. In this study, we assembled historical breeding records of seabirds throughout the Japanese archipelago and quantified the long-term population trends of 10 major breeding seabird species using a hierarchical Bayesian state-space model. The model revealed that six species had increasing or no detectable trends (Short-tailed Albatross Phoebastria albatrus, Leach’s Storm Petrel Oceanodroma leucorhoa, Pelagic Cormorant Phalacrocorax pelagicus, Japanese Cormorant Phalacrocorax capillatus, Spectacled Guillemot Cepphus carbo, and Rhinoceros Auklet Cerorhinca monocerata). However, decreasing trends were found not only in nationally threatened species (Common Murre Uria aalge, and Tufted Puffin Fratercula cirrhata) but also common species that are often described as abundant (Black-tailed Gull Larus crassirostris and Slaty-backed Gull Larus schistisagus). These declining species have declined to 3–35% of baseline levels over the past 30 years. This study provides the first evidence of long-term declines in common and widespread seabirds in Japan.