Background Human adenovirus 55 ( HA dV‐55) has caused recent outbreaks of acute respiratory disease ( ARD ) among adults and military trainees. The active surveillance for HA dV infections was sparse in China, and current knowledge on the HA dV‐type distributions and its molecular evolution is lacking. Objectives To acquire better understanding on the prevalence and molecular evolution of HA dV‐55 strains in China, for an informed strategy for disease control and prevention. Population/Methods Nasopharyngeal aspirates were collected from hospitalized children with ARTI in Chongqing during 2009–2012. The genotype of HA dV isolates were determined by sequencing the partial hexon and fiber genes. Whole genome sequences of HA dV‐55 were obtained for molecular evolution analysis. Results About 191 (8·55%) HA dV were detected in 2234 children, including 92 (48·2%) with HA dV‐7, 72 (37·7%) with HA dV‐3, 6 (3·1%) with HA dV‐55, 5 (2·6%) with HA dV‐5, 4 (2·1%) with HA dV‐1, 1 (0·5%) with HA dV‐2, and 11(5·8%) with untyped HA dV. Four of these children developed pneumonia, two of whom were diagnosed with severe pneumonia and/or encephalopathy. HA dV‐55 isolates clustered with HA dV‐11 sequences based on the hexon gene and clustered with HA dV‐14 sequences based on the fiber gene and the whole genome. The overall evolutionary rates of hexon gene, fiber gene, and whole genome of HA dV‐55 were estimated at 6·2 × 10 −5 s/s/y, 8·0 × 10 −5  s/s/y, and 1·7 × 10 −5 s/s/y, respectively. Conclusions This study suggested HA dV‐55 as an emerging infectious disease pathogen has conserved genetic structure and is closely related to each other. Further molecular investigation based on HA dV‐55 of wider origin might facilitate understanding its diversity, dissemination, and transmission in China.