Sheep and goats are important agriculture animals in Egypt. Mycoplasma is the most frequent causes of morbidity, mortality and economic losses associated with sheep and goats. Three mycoplasma species were obtained in this study from sheep and goats at Cairo abattoirs These mycoplasmas were found either as mixed or single infections and identified by biochemical and growth inhibition (GI) tests Mycoplasma isolates were classified into three biochemical groups group (1) contained 12 isolates (33.33%) from sheep and 6 isolates (23.1%) from goats (M. agalactiae). Group (2) contained 12 isolates (33.33%) from sheep and 10 isolates (38.5%) from goats (M. ovipneumoniae). Group (3) contained 12 isolates (33.33%) from sheep and 10 isolates (38.5%) from goats (M.arginini). PCR technique was found to be much faster than conventional microbiological techniques for isolation and identification and results could be obtained within five hours. In our study, six field isolates of M. agalactiae were tested by PCR, the results had confirmed that the field isolates were M. agalactiae by the presence of specific single band at 360 bp in each of field isolates and M. agalactiae reference strain Also PCR amplification of M. ovipneumoniae strains gave a characteristic band at 1070 bp. Six field isolates were tested for detection of M. arginini from sheep and goats and all of them gave a characteristic common band at 280 bp. The histopathological examination revealed that the severity of both sheep and goats infection with M. ovipneumoniae is greater than those infected with M. agalactiae and/or M. arginini .Lesions were mainly found in the lungs in the form of fibrinous pneumonia with pleuritis. Hepatocellular necrosis, lymphoid depletion in the spleen and bronchial lymph nodes as well as degeneratic changes and necrosis of the tracheal and intestinal epithelium.