Viral metagenomic analysis was used to identify a previously uncharacterized parvovirus species, "HBoV2," whose closest phylogenetic relative is the human bocavirus (HBoV). HBoV2 has a genomic organization identical to that of HBoV but has only 78%, 67%, and 80% identity, respectively, with the latter's NS1, NP1, and VP1/VP2 proteins. The study used polymerase chain reaction to detect HBoV2 sequences in 5 of 98 stool samples from Pakistani children and in 3 of 699 stool samples from Edinburgh. Nearly-full-length genome sequencing revealed the presence of 3 HBoV2 genotypes and evidence of recombination between genotypes. Further studies are necessary to identify anatomical sites of HBoV2 replication and potential associations with clinical symptoms or disease.