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Birds act as intermediate or definitive hosts of cyst-forming coccidia parasites of the genus Sarcocystis Lankester, 1882. However, the spectrum of species of Sarcocystis in birds and the role of the latter in the transmission of coccidia are still incomplete for many avian species including Tengmalm’s owl Aegolius funereus (Linnaeus, 1758). During a research of Tengmalm’s owls in Finland some fledglings were found dead and subsequently parasitologically examined. Therefore, this study is focused on the morphological and molecular description of a new Sarcocystis species found in the intestine of the Tengmalm’s owl and its possible role as definitive host. Methods Eleven fledgling owls from the Kauhava region of west-central Finland were found dead and subsequently were submitted for necropsy, parasitologically examined through flotation-centrifugation coprological technique for the presence of oocysts/sporocysts of genus Sarcocystis by light microscopy. Wet mounts were used for the examination of muscle samples (breast, legs, heart). Polymerase chain reaction and nested-PCR were carried out by using primers for 18S rRNA, 28S rRNA, ITS1 region and cox1 genes. Results All eleven examined birds were parasitized by numerous sporocysts and oocysts in the intestinal mucosa scrapings (prevalence 100%). Sporulated oocysts and sporocysts measured 16.34 − 16.96 × 11.47 − 12.09 µm and 11.85 − 13.52 × 7.77 − 9.25 µm, respectively. Skeletal and heart muscles were negative for sarcocysts. The phylogenetic analysis revealed that Sarcocystis funereus sp. nov. is closely related to Sarcocystis strixi from the barred owl ( Strix varia Barton, 1799) from the USA and Sarcocystis sp. isolate 5 from the European shrew ( Sorex araneus Linnaeus, 1758) from the Czech Republic, but a valid species. Conclusions This work provided the first and the most comprehensive record on Sarcocystis from owls obtained in Finland, thus highlighting the importance of molecular data in the species identification. Inglés