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A lake sediment profile spanning the last ~3200 years from Laguna Zoncho in the southern Pacific region of Costa Rica was analyzed for sub-fossil chironomids. Notable shifts in chironomid assemblages occurred during the late-Holocene. A distinct chironomid community, dominated by Tanypodinae such as Procladius and Labrundinia, appeared after ~550 cal. yr BP (~1400 CE). Prior to this time, the chironomid assemblage was more diverse, with taxa such as Paratanytarsus, Tanytarsus type N, and Cladotanytarsus important constituents of the chironomid community. A chironomid-based inference model for mean annual air temperature (MAAT), developed using partial least squares (PLS 2-component), was applied to sub-fossil chironomid assemblages from Laguna Zoncho to reconstruct late-Holocene thermal variability for the region. The key findings from this study are as follows: (1) chironomid-inferred MAAT at ~2740–1220 cal. yr BP (790 BCE–730 CE) was 1.2°C higher than the late-Holocene (~3200 cal. yr BP to present in this study) average of 21.3°C; (2) MAAT at ~470–90 cal. yr BP (1480–1860 CE) was 1.3°C lower than the late-Holocene average, potentially reflecting ‘Little Ice Age’ (LIA) cooling; and (3) evidence for an extended period of low lake levels between 1220 and 840 cal. yr BP (730–1110 CE) possibly indicated the influence of the Terminal Classic Drought (TCD) in southern Costa Rica. This study pioneers the use of sub-fossil chironomid remains to develop quantitative estimates of Holocene thermal variability and environmental change in Central America.