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To identify the subsidence induced by an offshore earthquake, chemical compositions, fossil assemblages, and radiocarbon ages of organic materials were analyzed for Holocene sediments in the Miyazaki Plain, southwest Japan. The lower sedimentary facies (SF1) composed of sand‐ and pumice‐rich sediments and the upper sedimentary facies (SF2) composed of silt‐rich sediments were identified by stratigraphical description. Sharp facies changes and sediment disturbances are observed in the boundary between SF1 and SF2. Diatoms of brackish and marine water origins, foraminifers, ostracods, and mollusks are common in SF2, while fossils are rare, and most of them are diatoms of freshwater origins in SF1. The stratigraphical and paleontological evidences suggest an environmental change from the lower terrestrial to the upper shallow marine. The change is laterally continuous and seems to be inconsistent with Holocene uplift trends in the Miyazaki Plain. Radiocarbon ages of organic matters and the occurrence of the Sakurajima–Bunmei tephra (1471–1476 ad) show that the environmental change could be attributed to local subsidence due to the 1662 Kanbun Hyuganada Sea earthquake shown in historical records. The chemical analysis shows clear contrast between SF1 and SF2 in terms of concentrations of cations and anions commonly rich in seawater (i.e. Na+, Mg2+, K+, Ca2+, Cl−, and SO42−) in adsorbed water extracted from the sediments, and total S concentrations in bulk sediments, supporting the environmental change from terrestrial to shallow marine. However, the bulk chemical composition, except total sulfur, remains rather unclear for use as marine‐derived chemical markers compared to the adsorbed water, because it is more affected by the composition of the source sediments. [ABSTRACT FROM AUTHOR]