This dataset describes the presence of Echinococcus multilocularis and Taenia taeniaformis in muskrats (Ondatra zibethicus) in Flanders, Belgium. From 1994 onward, muskrats from Flanders have been autopsied with the aim of understanding their demography. In 2008, we first detected EM in a muskrat from Lessines (Wallonia), just across the border with Flanders. Therefore, from 2009 onward, all available muskrats from Flanders and neighbouring regions were collected and examined. The dataset contains the following variables: date: YYYY-MM-DD province: Flemish province where the muskrat was captured, for locations outside of Flanders only a municipality is provided municipality: the municipality where the muskrat was captured weight: the weight of the animal in grams sex: either M: male or F: female taen: Infection with Taenia taeniaformis, scored as: 0: No T. taeniaformis present 1: Few T. taeniaformis present 2: Multiple T. taeniaformis present 3: A high number of T. taeniaformis present EM: Infection with Echinococcus multilocularis, scored as: N: negative, no parasites present P: positive, parasite present ?: unsure