Archaeological radiocarbon dating in coastal northern Hokkaido is challenged by the marine reservoir effect and the scarcity of materials with terrestrial carbon sources. This has contributed to gaps and general uncertainty in the timing of the region's culture-historical periods. The Late Holocene site of Hamanaka 2 on Rebun Island, featuring a stratified shell midden context with excellent preservation of organic remains, provides an ideal setting for addressing this issue. A Bayesian chronological model was deployed to study the timing of the site using a series of radiocarbon-dated macrobotanical samples. This resulted in narrowed-down estimated ageranges in eight of thirteen phases examined, providing the site with a more accurate radiocarbon chronology than before. These temporal data were consequently integrated with local palaeoecological evidence, revealing synchrony between cultural chronology and human-induced landscape transformations. The study demonstrates that the technique should permit more efficient building of archaeological chronologies in similar maritime environments.