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The last glacial-interglacial transition encompassed rapid climate oscillations that affected both hemispheres. At low latitudes, the pattern of oscillations is not well established. To address this issue, pollen analysis was performed at Cienega San Marcial, a monsoon-influenced site located on the southeastern edge of the Sonoran Desert at the limit of the tropical thornscrub. The pollen record covers the Late Wisconsinan glacial termination II, from 15650 to 13400cal. a BP, including GS-2 and the Lateglacial interstadial, and a recent historical period (AD c.1919 to 2004). We applied the modern analogue technique, in which pollen taxa are assigned to plant functional types (PFTs), to reconstruct the past climates. At the end of GS-2, a Juniperus-Pinus woodland is indicative of annual temperatures 10 +/- 2 degrees C colder than present and higher annual precipitation dominated by winter rains. The onset of the Lateglacial interstadial occurs at c.15500cal. a BP, resulting in a lower sedimentation rate and the spread of a xeric grassland. This period is associated with an increase in summer insolation. A weak signal of summer monsoon intensification is dated to 14825cal. a BP but is associated with colder winter temperatures. A wider spread of tropical taxa occurs after 13800cal. a BP, along with the loss of Juniperus, suggesting a temperature increase of approximately 3 degrees C. In spite of the earlier Lateglacial warming, the transition from glacial to interstadial conditions seems to be related to North Atlantic atmospheric variations. We conclude that during the last glacial-interglacial transition, the Sonoran Desert at 28.5 degrees latitude was sensitive to climate variations originating in northern latitudes. The recent historical sequence displays summer-dominant precipitation and additional drivers of climate change, including anthropogenic factors and El Nino, thus showing a stronger Pacific circulation influence in the subrecent period.