Fracture fillings in rock contain useful information on paleo-hydrogeology. Rock fractures filled mainly with carbonates are frequently observed on coastal outcrops of granite and sedimentary rock on Yakushima Island, Japan. From our previous studies, it was revealed that the ages of the fracture fillings which were 17 samples collected from 6 fractures in both rocks were 2,460-5,130 yrBP. As these are younger than the age of uplifted corals on Yakushima Island, it can be speculated that the fillings were precipitated in rock fractures after the corals were uplifted. However, their precipitation processes are uncertain. The present study performed microscopic observation and radiocarbon dating of fracture fillings that were collected from a single fracture in both rocks. In addition, the causes of age variations of fracture fillings were investigated to reveal the precipitation processes. Microscopic observation indicated that the fillings contain not only cementing materials, but also lithic fragments from the host rock and bioclasts. The results also showed that the fillings have layered structures. Radiocarbon dating revealed that there is a 2,000-3,000 year variation even in samples that were collected from a single fracture. This might be caused by not only altitude of samples but also layered structures, which indicate multiple precipitation events. On the other hand, the effect of bioclasts on the ages of fracture fillings was not significant as their content was relatively low.