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• The genetic diversity of feline bocavirus in the Anhui Province is significant. • Recombination analysis showed that inter- and intra-genotype recombination events had occurred. • FBoV-1 and FBoV-3 are continuously evolving toward adaptation. • Selection pressure is the main factor for codon usage bias during evolution. To understand the epidemic status of feline bocavirus (FBoV) in Anhui Province, eastern China, FBoV was successfully extracted from fecal samples of domestic cats, and five complete genomes were amplified in this study. Phylogenetic analysis showed that these five strains belong to three different FBoV genotypes. Recombination analysis showed that inter- and intra-genotype recombination events occurred. Selection pressure and codon usage bias analyses indicated that FBoV-1 and FBoV-3 continuously evolve toward adaptation, and selection pressure is the main factor for codon usage bias during evolution. This study provides the first molecular evidence of FBoV prevalence in eastern China, further enriching the available information on its genetics and evolutionary characteristics and providing a basis for further research on its evolution. [ABSTRACT FROM AUTHOR]