Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state east of the confluence of the old Mlava and the Danube rivers (Serbia). The vessels were found in the ground that used to be river sediment and were temporarily stored within the semi-underground exhibition space of Mammoth Park. As part of the pre-conservation investigations, the primary aim of the research presented was to characterize the culturable mycobiomes of two excavated wooden artifacts so that appropriate conservation procedures for alleviating post-excavation fungal infestation could be formulated. Utilizing culture-based methods, a total of 32 fungi from 15 genera were identified, mainly Ascomycota and to a lesser extent Mucoromycota sensu stricto. Soft-rot Ascomycota of genus Penicillium, followed by Aspergillus and Cephalotrichum species, were the most diverse of the isolated fungi. Out of a total of 38 isolates, screened on 7 biodegradation plate assays, 32 (84.21%) demonstrated at least one degradative property. Penicillium solitum had the highest deterioration potential, with a positive reaction in 5 separate plate assays. The obtained results further broaden the limited knowledge on the peculiarities of post-excavation soft-rot decay of archaeological wood and indicate the biochemical mechanisms at the root of post-excavation fungal deterioration.