| Summary: | Forest musk deer (Moschus berezovskii) is an endangered, protected species in China. Intestinal coccidiosis is a significant problem for captive forest musk deer. However, there are few reports on the prevalence and molecular characteristics of Eimeria sp. in forest musk deer. We sought to investigate the prevalence of Eimeria sp. in forest musk deer in the Sichuan and Shaanxi provinces in China. We also investigated the molecular characteristics of Eimeria sp. by analyzing the 18S rRNA gene. We collected a total of 328 fecal samples from forest musk deer on seven farms throughout the Sichuan and Shaanxi provinces. We extracted this parasite’s DNA and used this as a template for nested PCR amplification. The 18S rRNA gene fragment was associated with the plasmid vector, and these products were introduced into Escherichia coli (DH5α). The cultured bacterial solution was used as a PCR reaction template for identification purposes. We collected 328 fecal samples from forest musk deer in Lixian (n = 54), Maoxian (n = 52), Ma’erkang (n = 49), Dujiangyan (n = 55), Hanyuan (n = 41), Luding (n = 36) and Weinan (n = 41). One hundred ninety-eight (60.37%) fecal samples tested positive for Eimeria sp. . In our analysis of the 18S rRNA gene we found 34 types of Eimeria sp. with a similarity of 90.5–100%. We constructed a phylogenetic tree based on the parasite’s 18S rRNA gene sequence. Our findings indicated that the Eimeria sp. that parasitized the intestinal tract of forest musk deer was closely related to Eimeria alabamensis from Bos taurus and Eimeria ahsata from Ovis aries. To the best of our knowledge, ours was the first investigation and molecular identification of Eimeria sp. sampled from captive forest musk deer in China. Our results provide epidemiological data for the monitoring and prevention of Eimeria sp. in captive forest musk deer.
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