In recent years, deep drilling undertaken as part of the International Continental Drilling Program has generated multiple long lacustrine sedimentary records to reconstruct continental paleoclimate. In many cases, the tectonic and geomorphic history of these basins is under-constrained and poorly known, which affects the interpretation of climate history from geophysical, geochemical, and paleobiotic proxies in the sedimentary record. In addition, non-analog biotic assemblages that reflect evolutionary processes may constrain the reconstruction of past environments. In the drill-core record of Lake Titicaca, spanning the last ~. 370. ka, the diatom stratigraphy reflects both the influence of climate and the long-term evolution of the lake basin and its biota. In the upper part of the drill-core sequence, glacial intervals were deep and dominated by freshwater planktic taxa, and peak interglacial intervals were shallow and dominated by benthic species, some with saline affinities. In the basal sections of the drill-core record, benthic diatoms are dominant in both glacial and interglacial units, with freshwater taxa dominating the glacial strata. This suggests that the ancient lake basin was shallower during intervals of both wet and dry climate, and that the modern deep lake may result from a progressive subsidence and deepening of the basin over time. In addition, morphological evolution in one of the major lineages of planktic diatoms, Cyclostephanos, indicates substantial change in the limnological environment that affected species morphology and may have driven speciation. © 2011 Elsevier B.V.