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Small mammals are an important group of wildlife that can transmit pathogens to humans and animals. There is a lack of comprehensive studies on the protozoan parasites of the genus <i>Sarcocystis</i> in agricultural areas. The aim of the current research was to evaluate the prevalence of <i>Sarcocystis</i> spp., and to identify the parasite species found in the skeletal muscles of rodents and insectivores from commercial orchards. A total of 679 muscle samples from small mammals, mainly rodents (n = 674), belonging to eight species were examined. Muscle samples were pooled into groups, then digested, and the presence of the <i>Sarcocystis</i> species was confirmed by molecular methods. The examined parasites were determined in five rodent species, <i>Apodemus agrarius</i>, <i>A</i>. <i>flavicollis</i>, <i>Clethrionomys glareolus</i>, <i>Microtus arvalis</i>, and <i>M</i>. <i>oeconomus</i>. The prevalence of <i>Sarcocystis</i> spp. was low: 2.23% in voles and 0.79% in mice. Based on a sequence comparison of <i>cox1</i> and <i>28S</i> rDNA, four species were identified: <i>S</i>. <i>myodes</i>, <i>Sarcocystis</i> cf. <i>strixi</i>, <i>Sarcocystis</i> sp. Rod1, and <i>Sarcocystis</i> sp. Rod2. This is the first report of <i>S</i>. <i>myodes</i> in <i>A</i>. <i>agrarius</i>, <i>A</i>. <i>flavicollis</i>, and <i>M. arvalis</i>. The identified species were most closely related to <i>Sarcocystis</i> spp., and were transmitted by predatory mammals and birds. Future studies are needed to describe the species morphologically, as well as to define the host spectrum and to evaluate their possible pathogenicity.