Simple SummarySmall mammals not only play an important role in ecosystems, but they also can transmit a wide range of pathogens to humans and domestic animals. The data on protozoanSarcocystisparasites in orchard-dwelling small mammals are still scarce. Members of the genusSarcocystisform sarcocysts in the muscles of intermediate hosts and develop sporocysts in the intestines of definitive hosts. In the present study, 679 muscle samples of small mammals, collected in commercial orchards and berry plantations in Lithuania, were screened forSarcocystisparasites via DNA analysis. The prevalence ofSarcocystisspp. was low as only nine pooled muscle samples were found to contain the parasites examined. Four species were identified in the examined small mammals, including two potentially newSarcocystisspecies that were detected in the muscles of voles. The phylogenetic results suggested that birds and mammals are the definitive hosts of theSarcocystisspp. identified in the current study.AbstractSmall 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 genusSarcocystisin agricultural areas. The aim of the current research was to evaluate the prevalence ofSarcocystisspp., 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 theSarcocystisspecies was confirmed by molecular methods. The examined parasites were determined in five rodent species,Apodemus agrarius,A.flavicollis,Clethrionomys glareolus,Microtus arvalis, andM.oeconomus. The prevalence ofSarcocystisspp. was low: 2.23% in voles and 0.79% in mice. Based on a sequence comparison ofcox1and28SrDNA, four species were identified:S.myodes,Sarcocystiscf.strixi,Sarcocystissp. Rod1, andSarcocystissp. Rod2. This is the first report ofS.myodesinA.agrarius,A.flavicollis, andM. arvalis. The identified species were most closely related toSarcocystisspp., 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.