AbstractEnterovirus C96 (EV‐C96) is a recently discovered serotype belonging to enterovirus C species. It had been isolated from patients with acute flaccid paralysis, hand, foot, and mouth disease, diarrhea, healthy people, or environmental specimens. Despite increasing reports of the virus, the small number of full‐length genomes available for EV‐C96 has limited molecular epidemiological studies. In this study, newly collected rare EV‐C96 strains in China from 1997 to 2020 were combined with sequences available in GenBank for comprehensive analyses. Sequence analysis revealed that the nucleotide sequence similarity of EV‐C96 and the prototype strain (BAN00‐10488) was 75%–81.8% and the amino acid sequence similarity was 85%–94.9%. EV‐C96 had a high degree of genetic variation and could be divided into 15 genogroups. The mean evolutionary rate was 5.16 × 10−3 substitution/site/year, and the most recent common ancestor was dated to 1925. A recombination analysis revealed that EV‐C96 may be a recombinant derived from other serotypes in the EV‐C group in the nonstructural protein coding region. This comprehensive and integrated analysis of the whole genome sequence of EV‐C96 provides valuable data for further studies on the molecular epidemiology of EV‐C96 worldwide.