Influenza viruses pose significant public health challenges, causing seasonal epidemics with high morbidity and mortality. This study sequenced influenza viral RNA from hospitalized patients with severe acute respiratory illness in Sri Lanka using an amplicon-based approach on the Illumina platform. Raw sequencing reads were quality checked using FASTP and Trimmomatic. Assembly was performed with SPAdes, and subtype identification was conducted using ABRIcate. Phylogenetic trees for HA and NA genes were generated in MEGA X and Geneious Prime and visualized with iTOL. Data analysis was performed using Galaxy and INSaFLU. Nineteen patient samples from different regions were successfully sequenced, identifying influenza A H1N1 (7/19), H3N2 (6/19), and influenza B (6/19). Notably, co-infection with H1N1 and the SARS-CoV-2 Omicron variant was observed, along with the co-circulation of influenza A H1N1, H3N2, and B strains in 2023. Molecular analysis revealed that all H1N1 and H3N2 strains carried mutations consistent with global strains. Influenza B strains also aligned with global trends. Key mutations affecting antigenicity and receptor binding were identified, highlighting viral evolution. This study explores the molecular evolution of influenza viruses in Sri Lanka (2021–2024) post-COVID-19. Findings underscore the need for continued molecular surveillance to inform public health strategies, particularly regarding co-infections and emerging mutations. However, this study did not assess the association between influenza genomic characteristics and disease severity; thus, future research could explore potential links between specific mutations, clades, or co-infections and clinical outcomes.