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The improved fluorine analysis method by ion chromatography was applied to the fossil human bones excavated from the Shiraho‐Saonetabaru Cave site on Ishigaki Island, which were dated back to the Late Pleistocene. This study presents the first systematic results on individual variation of F/P ratios of fossil bones using less than 1 mg samples. In addition to the burial period, the F/P ratio was governed by the local difference in seepage water circulation, because dripping water in a cave slowly flowed through the sediment and fluorine accumulated in the bone from the water. The F/P ratios provide a powerful tool for elucidating the burial situation and subsequent depositional environment. The average F/P ratio was well correlated with the 14C age of the samples. The present method can be practically applicable as a rough chronological classification of the Holocene and Pleistocene groups of human bones at this site. The only exception was the lower F/P values of the Pleistocene human skeleton belonging to Shiraho No. 4, which is thought to have been placed in a narrow space under the fallen rocks. [ABSTRACT FROM AUTHOR]