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Taiwan is particularly sensitive to changes in monsoonal precipitation and to typhoon-induced heavy precipitation events, however, rainfall variability in Taiwan on centennial and millennial time scales during the Holocene has not been well understood. This study describes mid-Holocene rainfall features of Taiwan based on pollen, total organic carbon (TOC), total nitrogen (TN), and C/N ratio records of core MD05-2908. The step-wise increase in sedimentation rate, fern spore percentage and concentration, TOC content, and C/N ratio suggests an increasing terrestrial material supply due to the intensified rainfall in Taiwan since 6800 cal. yr BP. This rainfall pattern shows an inverse pattern to the decreasing East Asian summer monsoon (EASM) strength represented by the multi-proxy records from North China. Variation of the East Asian summer circulation and associated moisture transport may account for the long-term rainfall changes in Taiwan. Superimposed on this trend, we interpreted three prominent rainfall changes, which focus on the periods of 6800–6600, 1090–880 and 490–190 cal. yr BP. These centennial time scale rainfall variations in our records are linked to the intensity of El-Nino Southern Oscillations.