A new isolate of chicken anemia virus (CAV) was designated GD-1-12. GD-1-12 was isolated from a 12-day-old commercial broiler in Guangdong province, China, in 2012. The GD-1-12 CAV caused high mortality, severe anemia, thymic atrophy, and subcutaneous hemorrhage in commercial broilers. Here, we report the complete genome sequence of GD-1-12 CAV and comparison with the complete genome sequence of another CAV that was isolated from human fecal samples in China (GenBank accession no. JQ690762). The genomes of the two CAV isolates shared high homology, although a deletion was identified by comparison. The findings from this study provide additional insights into the molecular characteristics of the CAV genomes and should advance knowledge for continuous monitoring and, perhaps, preventing the spread of the virus in chickens as well as in humans.