Highlights: • Lipid fingerprinting of modern biota helps reconstructing past environments. • Dry climate in YD recorded by Sphagnum retreat. • Pluvial episode suggested around 5,000 B.P. • Upper limit of Pinus mugo zone never passed over 1880 m.a.s.l. in Tatra Mts. • Lithophytic lichen biomass deposits with millenial delay. Sediments of two alpine lakes in Tatra Mts., Slovakia, record the environmental history of their catchments from deglaciation in Late Glacial warming up to the Subboreal period. We present a biomarker-based reconstruction of changes in the surrounding biota of two contrasting lakes – a relic lake in open fen Trojrohé pleso (TROJ) and a tarn lake Batizovské pleso (BAT). Taking advantage of young unaltered sediments, well-known source area, and main biomass producers, we used an actualistic approach and interpreted sedimentary lipid distributions using fingerprints of modern plant groups. Four chemostratigraphic units were defined in TROJ lake and five units in BAT lake, with boundaries and environmental changes roughly conforming to paleoclimatic intervals of the Holocene. The dry climate was recorded in the period 13,200 BP–11,500 BP, coincident with Younger Dryas stadial. In the sediment of TROJ lake at ca. 5,200 BP a sharp spike in the abundance of the aromatic terpenoid retene, decoupled from the trend of other abietane-type diterpenoids, may best be explained by episodic flooding due to the rise of the water table. Diploptene as a biomarker for bacterial activity is suggested to indicate the development of soil cover at the end of the B/A interstadial and its gradual increase in abundance in the Holocene most reflecting an extension of vegetated area and more complex development of soil cover. Based on the absence of conifer biomarkers in the sediments of BAT lake, the upper limit of the continuous Pinus mugo scrub never reached the altitude of 1880 m a.s.l. between 16,247 and 4,420 BP, whereas conifer canopy was permanently present around TROJ lake at 1611 m a.s.l. between 10,439 and 3,113 BP.