History of variability of tropical cyclones (TC) in the North-Western Pacific is critical for understanding impacts of future climatic changes. Natural archives of paleo-typhoon variability can be used to assess how changes in the planetary climatic system during the Holocene could influence TC frequency and intensity in this part of Pacific. Extreme typhoon-related rains are the main cause of catastrophic floods on Sakhalin Island and deposits of these floods are evidence of paleo-typhoon. The paleo-typhoons that triggered extreme floods on Southern Sakhalin during the last 6.6 kyr are recorded in the sequence on the interfluvial surface in the northern Susunay Lowland (Naiba River basin). The sequence includes peat bog with numerous loam interlayers deposited during extreme floods inundating the bog. We reconstructed paleo-environmental conditions, including humidity and flood activity, based on analysis of diatoms. We found biological indicators that point to the past floods. The mineral content in the peat being one criteria indicative of the high frequency of floods. The peat bog developed in place of a lagoon that existed at the maximum phase of the Holocene transgression. Peat accumulation began in the freshened lagoon coast ~6010 cal yr B.P. When sea level dropped, the lagoon turned into a coastal lake (~5710–5040 cal yr B.P.). A swamp formed in place of the lake under varying moisture conditions. We identified and dated 25 extreme floods and assessed the paleoclimatic background of the events. A recent catastrophic flood from typhoon Phyllis (1981 CE) is considered as an analogue of the paleo-events. The frequency of extreme typhoons increased both during warm (wet and dry) phases and in cold dry phases of the climate fluctuations. We identified three periods of a high typhoon activity (4640–4360; 4030–3580; 1860–1380 cal yr B.P.), when super-typhoons came onto the island once every 30–90 years. A comparison between the extreme typhoons in the south of Sakhalin and in the Sea of Japan region show both synchronism and metachronism of the periods of typhoon activity. Instrumental measurements during 20th–21st centuries revealed considerable changes in super-typhoon tracks; a similar variability may be safely supposed in typhoon tracks in the past. To predict future tropical cyclone activity and the risk of floods under modern climatic instability it is necessary to understand factors influencing variability in the occurrence of strong typhoons and associated extreme floods events on a paleo-scale. This is especially important for areas with rapidly developing coastal economies and intensive use of gas and oil resources, such as Sakhalin Island.