Based on palynological study of the samples from the Late Pleistocene sediments from Moldova and from the Late Paleolithic Bolshaya Akkarzha site (southern west Ukraine), the various and numerous fungal palynomorphs (spores, hyphnodopodia and fruit-bodies) were identified. The taxonomic diversity and frequency of palynomorphs are varying in horizons. The frequent Glomus was encountered in the Upper Pleistocene loesses and paleosoils of the different natural outcrops in Moldova. The abundant Glomus was observed in loess corresponded to the Last (Würmian) Glacial period. The most diverse fungal palynomorph taxa of coprophilous fungi were established in the cultural layer of the archaeological site. The frequencies and taxonomic variety of fungal palynomorphs significantly decrease in Holocene sediments, but increase the quota of parasitic fungi (Helminthosporium and Coryneum). The predominance of Glomus spores are evidence for active erosive processes in the region where open xerophilous grasslands predominated. Represented results show the importance of fungal palynomorphs for palaeoecological reconstructions of the Quaternary.