Diseases of the respiratory system are common in all species of domestic animals, and there are many different factors acting together to cause the appearance of the disease which results in economical loss. This study was aimed to describe the prevalence of bacterial agents, isolation, identification, and molecular diagnosis in Duhok Province This study was conducted on 4061 slaughtered animals which were divided into sheep (3667) and ( 394) goats at Duhok abattoir, from September 2020 to September 2021. Two hundred fifty-three affected lungs were collected from slaughters of sheep and goats. Different media and biochemical tests were used for the isolation and identification of different types of bacterial species from affected lung samples. The results of bacterial isolation detected seven different species of gram-positive and negative bacteria. The result found that highest percentage rate was recorded with Staphylococcus aureus while lowest rate was with Pseudomonous spp they were identified by colony morphology and the traditional biochemical examination. In conclusion, the current study found that there were different species of bacteria that causes pneumonia in small ruminant at the Duhok abattoir.