The forests of the Siskiyou Mountains are among the most diverse in North America, yet the long-term relationship among climate, diversity, and natural disturbance is not well known. Pollen, plant macrofossils, and high-resolution charcoal data from Bolan Lake, Oregon, were analyzed to reconstruct a 17,000-yr-long environmental history of high-elevation forests in the region. In the late-glacial period, the presence of a subalpine parkland of Artemisia, Poaceae, Pinus, and Tsuga with infrequent fires suggests cool dry conditions. After 14,500 cal yr B.P., a closed forest of Abies, Pseudotsuga, Tsuga, and Alnus rubra with more frequent fires developed which indicates more mesic conditions than before. An open woodland of Pinus, Quercus, and Cupressaceae, with higher fire activity than before, characterized the early Holocene and implies warmer and drier conditions than at present. In the late Holocene, Abies and Picea were more prevalent in the forest, suggesting a return to cool wet conditions, although fire-episode frequency remained relatively high. The modern forest of Abies and Pseudotsuga and the present-day fire regime developed ca. 2100 cal yr B.P. and indicates that conditions had become slightly drier than before. Sub-millennial-scale fluctuations in vegetation and fire activity suggest climatic variations during the Younger Dryas interval and within the early Holocene period. The timing of vegetation changes in the Bolan Lake record is similar to that of other sites in the Pacific Northwest and Klamath region, and indicates that local vegetation communities were responding to regional-scale climate changes. The record implies that climate-driven millennial- to centennial-scale vegetation and fire change should be considered when explaining the high floristic diversity observed at present in the Siskiyou Mountains.