A new high-resolution pollen and NPP (non-pollen palynomorph) analysis has been performed on the sediments of Lake Dojran, a transboundary lake located at the border between Greece and the former Yugoslav Republic of Macedonia (FYROM). The sequence covers the last 12 500 years and provides information on the vegetational dynamics of the Late Glacial and Holocene for the southern Balkans. Robust age model, sedimentological diatom, and biomarker analyses published previously have been the base for a multi-perspective interpretation of the new palynological data. Pollen analysis revealed that the Late Glacial is characterized by steppic taxa with prevailing Amaranthaceae, Artemisia and Poaceae. The arboreal vegetation starts to rise after 11 500 yr BP, taking a couple of millennia to be definitively attested. Holocene vegetation is characterized by the dominance of mesophilous plants. The Quercus robur type and Pinus are the most abundant taxa, followed by the Quercus cerris type, the Quercus ilex type and Ostrya-Carpinus orientalis. The first attestation of human presence can be presumed at 5000 yr BP from the contemporary presence of cereals, Juglans and Rumex. A drop in both pollen concentration and influx together with a δ 18 O carb shift indicates increasing aridity and precedes clear and continuous human signs since 4000 yr BP. Also, a correlation between Pediastrum boryanum and fecal stanol suggests that the increase in nutrients in the water is related to human presence and pasture. An undoubted expansion of human-related plants occurs since 2600 yr BP when cereals, arboreal cultivated and other synanthropic non-cultivated taxa are found. A strong reduction in arboreal vegetation occurred at 2000 yr BP, when the Roman Empire impacted a landscape undergoing climate dryness in the whole Mediterranean area. In recent centuries the human impact still remains high but spots of natural vegetation are preserved. The Lake Dojran multi-proxy analysis including pollen data provides clear evidence of the importance of this approach in paleoenvironmental reconstruction. Cross-interpretation of several proxies allows us to comprehend past vegetation dynamics and human impact in the southern Balkans.