Abstract Human adenoviruses (HAdVs) are highly contagious and have significant clinical implications in the pediatric population. In the present study, we employed a combination of long-read sequencing and short-read sequencing to accurately reconstruct 32 genomes of HAdVs. The phylogenetic analyses based on the whole genome and genes revealed distinct sub-clusters within HAdV-B and -E. For HAdV-C, the phylogenetic trees constructed from hexon, fiber, and E3 gene sequences consistently matched the whole-genome phylogeny, reflecting the high sequence diversity in these regions. Notably, in regions with high sequence diversity, we observed a higher number of recombination breakpoints and lower GC content. Additionally, the E4 gene region of HAdV-C exhibited a Ka/Ks ratio > 1, indicating that positive selection may be driving the fixation of advantageous mutations. These genetic characterization analyses are crucial for enhancing future surveillance of HAdVs, facilitating a more strategic and proactive approach to monitoring their evolution, diversity, and epidemiological trends.