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.