Simple SummaryMembers of the genus Sarcocystis (Apicomplexa: Sarcocystidae) are protozoans that have a two-host, prey–predator life cycle. These parasites are most thoroughly examined in economically important animals. Several Sarcocystis species are known to form macroscopic and microscopic sarcocysts in the muscle tissues of sheep. A previous study carried out in Lithuania has shown a maximum Sarcocystis infection prevalence in sheep and a high parasite burden; however, species were not identified. In the present study, diaphragm, oesophagus, and heart samples of 69 sheep raised in Lithuania were examined. No macrocysts were detected in the sheep muscles, while the microcysts found corresponded to two morphological types. By molecular methods, two Sarcocystis species, S. arieticanis and S. tenella, using canids as their definitive hosts, were identified for the first time in sheep from Lithuania. Both species were detected in all the studied animals. In summary, very high detection rates of S. arieticanis and S. tenella ranging from 82.61% to 100% were established in the examined diaphragm, oesophagus, and heart muscle samples of sheep.Data on the distribution of different Sarcocystis species in various muscles of sheep are scarce. In the present study, 190 diaphragm, oesophagus, and heart muscle samples of 69 sheep raised in Lithuania were examined for the presence of Sarcocystis spp. Under a light microscope, two morphological types of microcysts corresponding to S. arieticanis and S. tenella were detected. Eight and 12 sarcocysts of S. arieticanis and S. tenella, respectively, were isolated and characterised by the sequencing of a portion of cox1. The sequence comparisons revealed the highest similarity between European and Asian isolates of S. arieticanis and S. tenella obtained from domestic sheep and other wild Caprinae hosts. Based on peptic digestion, nested PCR targeting cox1, and sequencing, a 100% infection prevalence of S. arieticanis and S. tenella was observed in the 69 studied animals. The occurrence of S. tenella was significantly higher in the diaphragm than in the oesophagus (χ2 = 13.14, p < 0.001), whereas differences in the prevalence of S. arieticanis in the studied muscle types were insignificant (χ2 = 1.28, p > 0.05). Further molecularly based epidemiological studies are needed to compare the prevalence of Sarcocystis species in various muscles of sheep raised in different geographic regions.