A 13,000-year history of late-Quaternary vegetational and climatic change has been derived from lacustrine sediments from Pleasant Island in the Glacier Bay region of southeastern Alaska. Early arrival of lodgepole pine and mountain hemlock, indicated by the presence of pollen and conifer stomata, suggests expansion from refugia in the Alexander Archipelago. A short-term climatic reversal, possibly correlated with the European Younger Dryas, is inferred from the expansion of tundra elements and deposition of inorganic sediments between 10,600 and 9900 14C yr B.P. Two peat cores from the lake catchment verify Holocene vegetation changes and aid in the separation of biogenic from climatic forces affecting vegetation history. Differences in pollen representation among the three cores illustrate the variation among pollen-collecting substrates, as well as the spatial heterogeneity of peatland development and its dependence on local hydrology. Initial peat accumulation and soil paludification, occasioned by increases in temperature and precipitation in the early Holocene, allowed western and mountain hemlock to replace sitka spruce 8500–8000 yr B. P. Open muskeg became widespread about 7000 yr B. P. and allowed lodgepole pine to reinvade the region after a 2000-yr absence. The extensive replacement of fen elements by bog taxa at 3400 yr B. P. suggests increased paludification due to changing hydrologic conditions; its correlation with the upland expansion of Tsuga heterophylla suggests the onset of a cooler/wetter Neoglacial climate in southeastern Alaska.