Cryptosporidium is an intestinal protozoan parasite prevalent in a wide range of mammals. Although it has been recorded in many hosts, its impact on endangered species is poorly understood. Here we present a preliminary study of four populations of the highly threatened spotted souslik (Spermophilus suslicus), living in the westernmost part of the species range. The populations inhabit fragmented habitats and suffer from loss of genetic variation. An IFA test revealed that 35.9% of sampled animals (41/114) was infected with Cryptosporidium and none with Giardia. The prevalence and infection intensity differed among the populations. In areas grazed by cattle it was about 3 folds higher, which suggests a possible transmission route. To the authors best knowledge the present study is the first report of Cryptosporidium infections in S. suslicus.