To investigate the phylogenetic and evolutionary analysis of porcine bocavirus (PBoV), 281 clinical samples including 236 intestinal tissue samples and 45 fecal samples were collected from diarrheal piglets in 27 different pig farms of central China, and SYBR Green I-based qPCR assays were developed to detect PBoVs. Among the 281 samples, 148 (52.67%) were positive for PBoV1/2, 117 (41.63%) were positive for PBoV3/4/5, and 55 (19.57%) were positive for both PBoV1/2 and PBoV3/4/5. Subsequently, two complete genome sequences of PBoV strains CH/HNZM (accession numbers KX017193) and PBoV-TY (accession numbers MH454686) were cloned in this study. A multiple genomic sequence alignment showed that the pairwise similarity of the two PBoV strains was 94.8%, and they had 44.5%-95.8% genomic nucleotide sequence identity with 35 reference strains. The phylogenetic analysis demonstrated that the two PBoV strains CH/HNZM and PBoV-TY clustered into the PBoV2 group, and PBoV-TY was closely related to the PBoV strain GD18 strain (KJ755666) which may be derived from PBoV strains 0912/2012 (MH558677) and 57AT-HU (KF206160) through the recombination analysis. Compared with reference strain ZJD (HM053694)-China, a higher variation in the NS1 amino acids of PBoVs was found for CH/HNZM and PBoV-TY. These results had provided further information of the PBoV prevalence in central China, and they extend our understanding of the molecular epidemiology and evolution of PBoV.