Two clusters of influenza?like illness (ILI) occurred during the winter of 2024-2025 at a dog breeding facility in Shangqiu, Henan Province, China. Clinical samples were collected and tested for influenza A virus (IAV), followed by whole?genome sequencing to characterize the epidemiological and molecular features of the causative viruses. A total of, 3,898 samples were obtained from 2,024 dogs, among which 708 tested positive for IAV. During both outbreaks, oropharyngeal swabs showed the highest positivity rates (59.03% and 25.26%), whereas anal swabs yielded the lowest (17.62% and 4.80%). All dogs with positive anal swabs also tested positive in oropharyngeal swab, indicating that viral replication was primarily localized to the respiratory tract. Among the positive samples, 376 yielded HA and NA gene sequences with >80% completeness. HA nucleotide identities ranged from 98.28% to 100.00%, and NA identities ranged from 99.00% to 100.00%. Phylogenetic analyses revealed that both HA and NA genes clustered within the post?2018 canine H3N2 lineage. The NA phylogeny further showed two distinct subclades, suggesting the potential involvement of multiple viral introductions. Frequent introduction of new dogs into the facility may have been a major driver of the sustained outbreaks. Establishing a surveillance system for canine influenza virus, along with early detection and intervention of outbreaks, will be essential for optimizing future prevention and control strategies against canine respiratory infectious diseases.