This study reports an outbreak of avian pox in a quarantine of canaries imported from Europe, with a mortality of 30% and clinical signs of dyspnea and blepharoconjunctivitis. During necropsy, beak cyanosis, serous blepharitis, caseous sinusitis, oropharyngitis, tracheitis, pulmonary edema, pneumonia, fibrinous airsacculitis, and splenomegaly were observed. Microscopically, edema, epithelial hyperplasia, hydropic degeneration, and vacuolated eosinophilic intracytoplasmic inclusion bodies were found; similar lesions were observed in the thymus, spleen, and other organs. The virus was isolated in chicken embryos, and it was identified and characterized using a sequence of 913 nucleotides of the DNA polymerase gene. Pathologic characteristics and molecular biology indicate the systemic presence of avian pox associated with an avipoxvirus of the B1 subgroup. Additionally, other lesions associated with Aspergillus sp., Macrorhabdus ornithogaster, and Isospora sp. were found, which could contribute to the high mortality. Canarypox virus should be considered a differential diagnosis in cases of dyspnea and high mortality in canary flocks.