Radiocarbon (14C) dating has been widely used to determine the age of deposits, but there have been frequent reports of inconsistencies in age among different dating materials. In this study, we performed radiocarbon dating on a total of 33 samples from 8-m-long sediment cores recovered from the wetland of the Muljangori volcanic cone on Jeju Island, South Korea. Ten pairs of humic acid (HA) and plant fragments (PF) samples, and three pairs of HA and humin samples, from the same depths were compared in terms of age. The PF were consistently younger than the HA. Interestingly, the age difference between HA and PF samples showed a long-term change during the past 8000 years. To test whether there was an association between this long-term age difference and climate change, we compared with the carbon/nitrogen (C/N) ratios and total organic carbon isotope (δ13CTOC) values of the sediments, as indicators of the relative abundance of terrestrial and aquatic plants; these parameters showed similar long-term trends. This suggests that the increasing (decreasing) trend in age difference was influenced by long-term dry (wet) climate change.