The members of the family Circoviridae are considered to be the smallest autonomously replicating viruses, including two genera, Circovirus and Cyclovirus. Circoviruses have been found in a variety of vertebrates, but whether they infect endangered protected animals has not been studied in much detail. Here, viral metagenomics and reserve PCR methods were used to detected and verified viral nucleic acid in the blood samples from giant pandas. According to these methods, the complete genome sequence of a novel circovirus, the Giant panda associated circovirus (GPCV) from the blood sample of three giant panda was identified. The GPCV genome is 2,090 bp in size and reveals two putative ambisense open-reading frames, encoding the major structural capsid protein and the replication associated protein, respectively, the latter having two predicted introns. Pairwise sequence comparison and phylogenetic analyses indicated GPCV was a putative new species within genus Circovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. It is the first time that circovirus has been identified from blood samples of giant pandas. These efforts will contribute to future analyses to illuminate the evolutionary relationships between classified and newly identified members of the family Circoviridae.