Black deposits covering speleothems, cave walls and floors in Postojna Cave and Predjama Cave (SW Slovenia), and charcoal found in soil outside the Postojna Cave, were studied in order to establish their origin and age. SEM/EDS analysis of these deposits from both caves indicated that they are charred plant remains, very similar to oxidised charcoal in soil. Stable carbon isotope δ13C values of −29.41‰ (Črna Jama, P1), −26.9‰ (Predjama), and −25.1‰ (charcoal in soil) confirm their origin from biomass burning. Radiocarbon dating from Postojna Cave (Črna Jama (P1) 8394±35calyrB.P. and Pisani Rov 8235±25calyrB.P.) suggests that the oldest analysed black deposits formed in the Early Holocene (Mesolithic). The age is consistent with soil charcoal found at 1m depth in the surrounding area. Black deposits from Predjama were dated to 4095±25calyrB.P. (Eneolithic) and were caused by burning fires at the cave entrance, as supported by archaeological remains. Prehistoric (2375±20calyrB.P.) charcoal from the upper part of the soil profile (0.5 to 0.6m) and historic (1240±29calyrB.P. or 745calyrCE) black deposits from Postojna Cave (Črna Jama, P2) are related to forest fires, which are most likely human-induced. We interpret the oldest dated black deposits in Postojna Cave as traces of Early Holocene natural forest fires, since fire activity inside Črna Jama and Pisani Rov is not supported by archaeological remains. Favourable cave entrance morphology and microclimate allowed smoke to enter the cave during the winter period and deposit on speleothems. But an anthropogenic cause of forest fires cannot be excluded, since there are well-documented Mesolithic archaeological cave sites located close to the area. The study shows that black deposits on speleothems in caves are an important palaeoenvironmental record and proxy for Holocene climate. Display omitted •Black deposits on speleothems and charcoal in soils in karst area were studied.•SEM/EDS, 14C dating, C stable isotope analysis, organic matter analyses were applied.•Black deposits and charcoal in soil proved forest fires event dating 8200calyrB.P.•Black deposits on cave speleothems are important proxy for Holocene climate.