BACKGROUND: In sheep, pneumonia is a major concern because of its high morbidity, mortality, and economic impact. It results from various infectious agents, including bacteria, viruses, and environmental stressors, that weaken the immune system. OBJECTIVE: The objective of this study was to monitor nucleotide sequence variations, gene expression, and serum biomarkers of inflammation and oxidative stress in sheep with pneumonia. Additionally, this study aimed to identify various bacterial strains and virulent gene combinations in pneumonic sheep, as confirmed by PCR. METHODOLOGY: The enrolled animals were categorized as follows: 50 apparently healthy ewes, considered the control group, and 150 infected ewes with pneumonia. The infected ewes included 100 sporadic cases from the Center for Sustainable Development of Matrouh Resources, Desert Research Center, Matrouh, Egypt, and 50 ewes from the slaughterhouse, all exhibiting respiratory symptoms such as coughing, serous to mucopurulent nasal discharge, fever, and abnormal lung sounds. Blood samples were collected to assess various biochemical parameters, detect SNPs, and analyse the expression of specific immunological and antioxidant-related genes. Nasopharyngeal and lung swabs were taken from the affected ewes for bacteriological analysis, and lung samples were collected for histological examination. RESULTS: Phenotypic characterization and identification revealed the presence of Klebsiella pneumoniae, Pasteurella multocida, Mannheimia haemolytica, Pseudomonas spp., Mycoplasma, Streptococcus, and Escherichia coli, with frequencies of 40%, 28.6%, 34%, 18%, 44%, 29.3%, and 20%, respectively. Additionally, virulence genes for Klebsiella pneumoniae, iutA and fimH, were detected at rates of 39% and 68%, respectively, whereas the toxA gene for Pseudomonas spp. was present in 59.2% of the cases. Nucleotide sequence variations in immunity- and antioxidant-related genes were observed between healthy and pneumonic ewes. The genes encoding IL-1α, IL1B, IL6, TNF-α, LFA-1, CR2, IL17, IL13, DEFB123, SCART1, ICAM1, NOS, and HMOX1 were significantly upregulated in pneumonia-affected ewes compared with resistant ewes. Conversely, the genes encoding IL10, SOD1, CAT, GPX1, and NQO1 were downregulated. Further analysis of the serum profile revealed a significant (P < 0.05) increase in IL-1α, IL-1β, IL-6, TNF-α, NO and MDA along with a significant (P < 0.05) decrease in the serum levels of C3, C4, CAT, GPx, GR and IL-10 in diseased ewes compared with healthy ewes. Histopathological examination revealed that the infected sheep exhibited broncho-interstitial pneumonia and purulent to fibrino-purulent bronchopneumonia. CONCLUSIONS: This study revealed the significant presence of various pathogens and virulence factors in infected sheep, along with distinct immunological and antioxidant gene expression patterns. The altered serum profile and gene regulation in pneumonia-affected ewes underscore the complex immune response and potential biomarkers for disease susceptibility and resistance.