Cryptosporidium spp. and Giardia spp. are wide-spread pathogens of humans and many species of mammals. The ways of transmission are very complex and difficult to define. Both parasites occur in similar environments and share a broad host range. However, in Poland there is still little known about the epidemiology of these parasites due to the paucity of data on human cases and only few studies in wildlife. The aim of our study was to determine the distribution of two intestinal protozoa in a few species of protected and game mammals in North-Eastern Poland. Additionally, we wanted to compare prevalence and abundance of these parasites between wild and farm animals, and to determine the species/genotypes of Cryptosporidium. Fecal samples collected from protected species (European beaver - 22, grey wolf - 14, European bison - 55, Polish Konik (horse) - 5) and game mammals (red deer - 52, roe deer - 22, boar - 5) were examined by IFA. We also studied a group of samples collected from farm animals: beaver - 30, red deer - 66, Polish konik - 5. Cryptosporidium oocysts were identified in 5 of 7 studied animal species (prevalence from 9% in roe deer to 36% in wolves), Giardia cysts in 4 of 6 studied species (prevalence from 1.7% in red deer to 7.7% in European beaver). Sequencing analysis of COWP gene fragment revealed that 5 Cryptosporidium isolates from wolves were C. parvum genotype 2 (zoonotic). The results show the important role of examined species in maintaining the natural sources of Cryptosporidium spp. and Giardia spp. infections in the environment.