Simple SummaryLittle is known about the distribution of rumen and liver flukes in sheep and goats in Germany or about the occurring rumen fluke species. These fluke infections can be detected by the parasite’s eggs in the host animal’s feces. Therefore, fecal samples from 223 sheep farms and 143 goat farms from northern and southern Germany were examined. The eggs of rumen flukes were detected on 2.2% of the samples, the eggs of common liver flukes on 2.7%, and the eggs of small liver flukes on 21.1% of the examined sheep farms. The rumen flukes were identified as the emerging species Calicophoron daubneyi. No rumen fluke eggs were detected on any of the goat farm samples, but common and small liver fluke eggs were detected in 5.6% and 7.0% of the goat herds, respectively. Differences in the geographical distribution of rumen and liver flukes between and within the two regions were identified. Rumen flukes were more frequently found in the north, while the two liver fluke species were more frequently found in the south of Germany. Sheep sharing the pasture with other ruminants were more likely to be infected with rumen flukes.Paramphistomidosis has recently been identified as an emerging parasitosis in Europe. This study estimated the prevalence of rumen flukes, Fasciola hepatica and Dicrocoelium dendriticum, in small ruminants in Germany and identified occurring rumen fluke species and potential predictors for fluke infections. Pooled fecal samples from 223 sheep farms and 143 goat farms in northern and southern Germany were examined by the sedimentation technique, and molecular species identification was performed on rumen-fluke-positive samples. In sheep, a flock prevalence of 2.2% was detected for rumen flukes. Calicophoron daubneyi was identified on four of five positive farms, while species identification failed in one flock. No rumen fluke eggs were detected in the examined goat herds. F. hepatica eggs were detected in 2.7% of the sheep flocks, while the herd prevalence was 5.6% in goats. Higher prevalence values of 21.1% (sheep) and 7.0% (goats) were observed for D. dendriticum. Mixed grazing with other ruminants and previously identified infections with rumen flukes and/or F. hepatica were identified as predictors for paramphistomidosis. The distribution of the three trematode species followed a geographical pattern associated with conditions favoring the relevant intermediate hosts. C. daubneyi is an established parasite in German sheep at a currently low prevalence.