A palynological investigation of the last glacial-interglacial cycle in the southern hemisphere tropical Andes reveals changes in the moisture balance as the main driver in vegetation change. Thirty accelerator mass spectrometry radiocarbon dates, biostratigraphy and tephra correlation reveal that a 119 m sediment core recovered from the Huiñaimarca sub-basin of Lake Titicaca (16.0° to 17.5° S, 68.5° to 70° W; 3810 masl) contains sediments covering > 151,000 years. Correlation of aridity indicators with precessional variations in insolation is used to fine tune the structure of the age-depth curve within this period.Variations in Isoëtes concentration (above/below 10,000 grains/cm3) identify the extent of shallow water environments. Examination of another palaeolimnological indicator (Pediastrum) and consideration of the bathymetry of the Huiñaimarca sub-basin allow the reconstruction of lake-level fluctuations. These data indicate five wet/dry cycles between c. 151,000 and 14,200 cal yr BP. High stands are suggested during the transition into (c. 134,000 cal yr BP), and out of (c. 114,000 and 92,000 cal yr BP), the last interglacial, and during full glacial conditions (c. 70,000 and 45,000 cal yr BP). These cycles are superimposed on a general trend of deepening lake levels through the glacial period.This interpretation is supported by correlation with sediments from Salar de Uyuni (20°S, 68°W; 3653 masl). The youngest wet episode is concurrent with palaeolake Minchin (c. 45,000 cal yr BP), with further evidence for an additional wet period commencing c. 28,000 cal yr BP, concomitant with palaeolake Tauca. The timing of lake level fluctuations is also supported by palaeoshoreline reconstructions from the Uyuni-Poopó region. However, our data do not suggest a major peak in lake level in Huiñaimarca during the Ouki lake cycle (c. 120,000–98,000 cal yr BP) as inferred from U–Th ages obtained from palaeoshorelines around Lago Poopó. The most extreme dry event occurs during the last interglacial period and resulted in a sedimentary hiatus tentatively dated to c. 121,000–129,000 cal yr BP.The observed wet/dry cycles are shown to have a marked and rapid impact on the vegetation. The aridity of the last interglacial promoted a community dominated by Chenopodiaceae/Amaranthacae, with no modern Andean analogue. Polylepis/Acaena pollen is also shown to fluctuate markedly (0–20%), particularly during the transitions into, and out of, the last interglacial. It is probable that this pollen taxon is primarily representative of the high altitude arboreal genus Polylepis, which is a key component of highly biodiverse Andean woodlands today. Rapid fluctuations indicate the sensitivity of this ecosystem to natural environmental pressure and potential vulnerability to future human impact and climate change.The 100,000 year (eccentricity) solar cycle is shown to be the major controlling factor in moisture balance and vegetation over the last glacial-interglacial cycle. However, significant fluctuations in moisture balance are also evident on timescales considerably shorter than the full glacial-interglacial cycle. We have linked these to precessional (21,000 year) forcing. Nevertheless, precise independent dating during the full glacial cycle is required to confirm the importance of this forcing mechanism.