This paper presents an original palaeoparasitological study performed on samples from a sedimentary core in a peat bog (Asi Gonia, White Mountains, Crete, Greece). The aim of the study is to test the preservation and concentration of parasitic remains in peat sediments, to discuss animal presence around the site throughout the record, and to compare the results with other biomarkers of environmental history. In this aim, 22 sediment samples distributed between the Roman period and the present were processed and the residues were observed under light microscopy in search of parasitic markers (microscopic eggs or oocysts). The majority of the samples (86.4%) tested positive for the presence of helminth eggs. Several taxa were observed throughout the studied period, including Trichuris sp., Ascaris sp., Capillaria sp., Fasciola sp., Paramphistomum sp. and Macracanthorhynchus sp. The assemblage of parasite markers changes throughout the record and the variations show close correlations with previously published grazing indicators (fungal spores) and vegetation changes (pollen grains). This study sheds lights on animal associations and changing environments in the watershed over the past 2000 years. Indeed, we detected three main phases consisting of: Roman animal herding with pigs in an evergreen oak forest, then a more irregular but almost constant presence of ruminants during a second Byzantine and modern phase in a heather maquis landscape and, finally, present-day grazing in a phrygana/steppe landscape. These results highlight how palaeoparasitology can contribute to multi-proxy approaches in peat bog sedimentary sequences.