Abstract: The molecular epidemiology on the mycoplasma pneumonia of sheep and the contagious caprine pleuropneumonia of goats in Fujian were investigated. A total of 61 samples from the goats with suspected infection of the diseases were collected from 6 regions in the province during 2014-2016. PCR with the mycoplasmatales primer as well as the specific primers for Mycoplasma ovipneumoniae, Mycoplasma mycoides subsp.capri, Mycoplasma capricolum Subsp. Capripneumonia, Mycoplasma capricolum subsp.capri, Mycoplasma arginin, Acholeplasma laidlawii and Mycoplasma agalactiae were applied for the detection.Part of the PCR positive clinical samples were selected to isolate Mycoplasma for subsequent cloning and sequencing based on their 16S rRNA. The detection rates on M. ovipneumoniae, M. mycoides subsp.capri, A. laidlawii and M. arginine were 73.77%(45/61), 6.56%(4/61), 6.56%(4/61) and 3.28%(2/61), respectively. The results suggested that the suspected contagious caprine pleuropneumonia in the province were mycoplasma pneumonia of sheep and goats caused mainly by M.ovipneumoniae. The finding would lead to effective prevention and treatment measures for the diseases.