Abstract. We compare eight pollen records reflecting climatic and environmental change from northern and southern sites in the tropical Andes. Our analysis focuses on the last 30 000 years, with particular emphasis on the Pleistocene to Holocene transition. We explore ecological grouping and downcore ordination results as two approaches for extracting environmental variability from pollen records. We also use the records of aquatic and shoreline vegetation as markers for lake level fluctuations and moisture availability. Our analysis focuses on the signature of millennial-scale climate variability in the tropical Andes, in particular Heinrich stadials (HS) and Greenland interstadials (GI). The pollen records show an overall warming trend during the Pleistocene–Holocene transition, but the onset of post-glacial warming differs in timing among records. We identify rapid responses of the tropical vegetation to millennial-scale climate variability. The signatures of HS and the Younger Dryas are generally recorded as downslope upper forest line (UFL) migrations in our transect, and are likely linked to air temperature cooling. The GI1 signal is overall comparable between northern and southern records and indicates upslope UFL migrations and warming in the tropical Andes. Our marker for lake level changes indicated a north-to-south difference that could be related to moisture availability. The air temperature signature recorded by the Andean vegetation was consistent with millennial-scale cryosphere and sea surface temperature changes but suggests a potential difference between the magnitude of temperature change in the ocean and the atmosphere. We also show that arboreal pollen percentage (AP %) and detrended correspondence analysis (DCA) scores are two complementary approaches to extract environmental variability from pollen records.