Fire-vegetation relationships are critical to understand transient mountain ecosystems and their long-term landscape dynamics, which is essential for alpine forest conservation. In this paper we aim to (1) reconstruct the Holocene fire history at high altitudes of the southern Central Pyrenees, (2) add evidence to the debate on fire origin, naturally or anthropogenically produced, (3) determine the importance of fire as a disturbance agent for sub-alpine and alpine vegetation, in comparison with the plant community internal dynamics applying conditional inference trees. We present and compare microcharcoal and pollen data series, from two lacustrine sedimentary sequences in the Central Pyrenees: Basa de la Mora (BSM), within the treeline ecotone at the sub-alpine belt (1914 m a.s.l.) and Marboré Lake, above the treeline at the alpine belt (2612 m a.s.l.). We evidence that, fire activity was not the most important factor in driving vegetation dynamics regionally. Our results suggest that spatially, the fire signal might be site-dependent while over time, climate exerted a strong influence on fire activity during the early-to-mid Holocene, showing more fires during the Holocene Thermal Maximum (HTM) (ca. 7000–6000 cal yr BP) whereas fire activity decreased with the cold Neoglacial period. At ca. 3700 cal yr BP, fire activity increased coinciding with a regional landscape opening, suggesting that human activities may have strengthened the importance of fire. Fire activity remained low over the last two millennia but a remarkable Holocene maximum for the last centuries in both sequences is observed, likely related to increasing human pressure.