Chronic bee paralysis virus (CBPV) is an important viral pathogen that affects adult bees. Although several CBPV strains have been reported, little information has been obtained from China. In this study, two major segments of the CBPV Chinese isolate CBPV-BJ, RNA 1 and RNA 2, were determined to be 3657 and 2267 nucleotides (nt) in length, respectively. RNA 1 and RNA 2 contained three and four open reading frames (ORFs), respectively, which agreed with known reference strains (EU122229 and EU122230). The RNA 1 had 98% nucleotide sequence identity to a known Chinese strain (KU950353), and RNA 2 had 97% nucleotide sequence identity to another Chinese strain (KU950354). Although the lengths of the RNA 1 and RNA 2 sequences were 17 nt and 38 nt shorter than those of the CBPV reference strains EU122229 and EU122230, respectively, the complete CBPV-BJ RNA 1 and RNA 2 sequences shared 91% and 92% identity with them. Phylogenetic analysis based on the sequences of the RNA-dependent RNA polymerase (RdRp) and putative structural proteins (pSPs) showed that CBPV-BJ was most closely related to the other two Chinese isolate (KU950353 and KU950354) and clustered with most Asian strains. These data provide new information that will lead to a better understanding of the diversity of the CBPV genome.