Background: Members of the genus Sarcocystis are protozoan parasites characterized by a prey-predator two-host life cycle. Sarcocysts are formed in muscles or CNS of the intermediate host (IH), while sporocysts develop in the small intestine of the definitive host (DH). Various birds of prey were confirmed to be DH for Sarcocystis spp. By contrast, only two species, S. wobeseri and S. falcatula were identified in the muscles of birds of prey. The latter species is pathogenic and can cause encephalitis in various birds. The aim of the present study was to identify Sarcocystis species in the muscles of birds of prey from Spain. Methods: In the period between 2019 and 2020, muscle tissues of 59 birds collected from Spain were examined for the presence of Sarcocystis spp. Sarcocysts in fresh squashed samples were morphologically characterised under a light microscope (LM). Sarcocystis species were identified by means of 28S rRNA and ITS1 sequence analysis. Results: With the help of methylene blue-staining microscopic sarcocysts were detected in 3/59 (5.1%) birds of prey from Spain. Under LM, one type of sarcocysts was observed. Sarcocysts were thread-like (1050–2160 × 130–158 μm), had a thin (0.7–1.4 μm) and smooth cyst wall. Septa divided the cysts into compartments filled with banana-shaped (5.9 × 1.7 μm) bradyzoites. On the basis of DNA sequence results, S. halieti was identified in the western marsh harrier (Circus aeruginosus) and the black kite (Milvus migrans) for the first time. Sarcocysts of S. halieti detected in the black kite and the western marsh harrier were shorter and wider as compared to those observed in the great cormorant (Phalacrocorax carbo) and the herring gull (Larus argentatus). Hence, S. halieti might infect birds belonging to three different orders, Suliformes, Charadriiformes and Accipitriformes. Conclusions: This is the first report of S. halieti in birds of prey as IH. Due to the inconsistency of research on Sarcocystis spp. from birds of prey, further complex morphological, histopathological, and molecular studies are required.