Background <p>Some of the most common pathogens in wildlife are parasites. Since wild cervids are phylogenetically close to a lot of our livestock species, disease dynamics can arise, for example, through shared parasites. Insight into regional patterns, shaped by ecosystems and cross-species relationships, is only slowly emerging and the species-specific knowledge about lifecycle and ecology of parasites is often based on cross-sectional studies and therefore limited. Possibilities for broad and easy investigation of parasites could be the key to widen our understanding of these systems and processes.</p> Methods <p>Here, shotgun metagenomics were investigated as a method for parasite detection in fecal samples of wild ungulates. The results were further validated by histopathological examination of gastrointestinal tissues.</p> Results <p>The results from the two methods are in line with similar studies, and while not being identical, complement each other.</p> Conclusions <p>This investigation revealed parasite composition and seasonal dynamics in two species of wild cervid red deer (<i>Cervus elaphus</i>) and roe deer (<i>Capreolus capreolus</i>).</p> Graphical Abstract <p></p>