Background: There has been considerable confusion concerning the number and classification of Sarcocystis spp. found in chickens. To date, no nucleotide sequences of Sarcocystis spp. from chickens have been provided in GenBank. The present study aimed to investigate the morphological and molecular characteristics of Sarcocystis spp. in chickens in China.Methods: Tissues from 33 chickens were collected in 2019. Sarcocysts were observed using light (LM) and transmission electron microscopy (TEM). Individual sarcocysts from different chickens were selected for DNA extraction, and five loci, 18S rDNA, 28S rDNA, the ITS-1 region (ITS-1), the mitochondrial cox1 gene (cox1), and the apicoplastic rpoB gene (rpoB), were amplified from each sarcocyst, cloned, sequenced and analyzed.Results: Only S. wenzeli was found in 14 of 33 (42.4%) chickens. Under LM, the sarcocysts were microscopic and exhibited palisade-like villar protrusions measuring 1.5–2.8 μm. The bradyzoites were lancet-shaped, measuring 9.2–12.6 × 1.5–3.5 μm. Ultrastructurally, the sarcocyst wall contained numerous stubby hill-like villar protrusions that were up to 1.2 μm long and 1.0 μm wide. The protrusions included scattered microtubules, which extended from the tips of the protrusions into the ground substance. The intraspecific similarity of the five loci (18S rDNA, 28S rDNA, ITS-1, cox1, and rpoB) among the newly obtained sequences ranged from 99.8–100%, 99.7–100%, 99.0–99.9%, 100% and 98.9–100%, respectively. The five loci showed different levels of interspecific sequence similarity with closely related species of Sarcocystis (e.g., 99.8%, 99.0–99.2%, 89.3-89.7%, 98.5%, and 97.5%, respectively, with S. anasi). Phylogenetic analysis based on three of the loci (18S rDNA, cox1, and rpoB) revealed that S. wenzeli formed an independent clade with Sarcocystis spp. that employ geese or ducks as intermediate hosts and canines as the known or presumed definitive host.Conclusions: The sequences of 18S rDNA, 28S rDNA, ITS-1, cox1 and rpoB from S. wenzeli reported here constitute the first records of genetic markers of Sarcocystis from chickens made available in GenBank. Based on sequence analysis, ITS-1 and rpoB are more suitable for discriminating S. wenzeli from closely related species of Sarcocystis. Phylogenetic analysis revealed that S. wenzeli presents a close relationship with Sarcocystis spp. from geese or ducks.