BackgroundHemotropic mycoplasmas (hemoplasmas) are emerging zoonotic pathogens with a worldwide distribution that can cause mild to severe hemolytic anemia, icterus, ill-thrift, infertility, and poor weight gain. However, understanding of the molecular epidemiology of hemoplasmas (Mycoplasma ovis and ‘Candidatus Mycoplasma haemovis’) is limited in sheep and goats, and the hemoplasma strain/species/variant ‘Candidatus M. haemovis’ was poorly studied throughout the world and had never been detected in China until now. Thus, the aim of the present study was to determine the molecular prevalence of hemoplasmas, including M. ovis and ‘Candidatus M. haemovis’ in sheep and goats from seven provinces and one autonomous region of China.MethodsA total of 1364 blood samples were collected from sheep and goats in seven provinces and one autonomous region of China. All blood samples were tested for hemoplasmas (M. ovis and ‘Candidatus M. haemovis’) by nested PCR amplification based on 16S rRNA gene. Positive specimens underwent nucleotide sequencing and phylogenetic analysis.ResultsOverall, 610 specimens (44.7%, 610/1364) were shown to be hemoplasmas (M. ovis and ‘Candidatus M. haemovis’) -positive by nested PCR amplification based on 16S rRNA gene. The prevalence in goats was 44.1% (379/860), and 45.8% (231/504) in sheep, while that in grazing small ruminants was 54.4% (396/728) and 33.6% (214/636) in house feeding small ruminants. Sequencing of the nearly complete 16S rRNA gene was successful for the 103 randomly selected positive specimens from different farms in different sampling sites of China. Among them, analysis of the 16S rRNA gene sequences identified M. ovis (n = 56) and ‘Candidatus M. haemovis’ (n = 47). Two (KU983740 and KU983746) of the four novel genotypes obtained in this study were closely related to M. ovis, while the other two genotypes (KU983748 and KU983749) had high identity with ‘Candidatus M. haemovis’. Remarkably, the genotype (KU983740) of M. ovis in sheep and goats in this study fell in a clade with two human hemoplasmas from USA (KF313922 and GU230144) and shared 99.8%–99.9% with them.ConclusionsIn this study, ‘Candidatus M. haemovis’ was first detected in Chinese sheep and goats and hemoplasmas (M. ovis and ‘Candidatus M. haemovis’) are highly prevalent, and widely distributed in China.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-017-1062-z) contains supplementary material, which is available to authorized users.