Background: Recently, it was proposed the name of Sarcocystis masoni n. sp. for the Sarcocystis that causes microcyst in skeletal muscle of South American camelids. However, there are no ultrastructural reports of microcysts of Sarcocystis in cardiac muscle of alpacas. This study reports ultrastructural features of microcysts of Sarcocystis sp. from cardiac muscle of naturally infected alpacas. Methods: Thirty alpacas (age range: three to five years) from the province of Junin, Peruvian Central Andes, were included in this study in January 2015. Cardiac muscle samples were evaluated by histology and transmission electron microscopy. Results: Bradyzoites in cysts had typical characteristics of Apicomplexa including organelles, a large nucleus, micronemes, dense bodies, and polysaccharide granules. Moreover, cysts had a thin wall with numerous, short, finger-like shapes with rounded tip protrusions (0.51 x 0.17 µm). Conclusion: Sarcocystis sp. from the heart and S. masoni n. sp. from the skeletal muscle have similar ultrastructural characteristics.