The purpose of this study was to molecularly characterize circoviruses that infect finches and gulls. Circovirus-specific DNAs were isolated using polymerase chain reaction methods from bursa of Fabricius tissues from a Gouldian finch (Chloebia gouldiae) and a herring gull (Larus argentatus) that were known to be circovirus-infected. Nucleotide sequence determination and analysis of cloned genomic DNAs showed that these circoviruses represented novel members of the genus Circovirus of the family Circoviridae, and have been tentatively named Finch circovirus (FiCV) and Gull Circovirus (GuCV). Both new circoviruses shared genome organizational features with previously characterized circoviruses, such that both contained two major, inversely-arranged open reading frames encoding the putative replication-associated and capsid proteins, and both contained a potential stem-loop and nonanucleotide motif. Phylogenetic analyses based on genome nucleotide sequences and involving the seven additional genus members indicated that FiCV and GuCV were more closely related to canary circovirus, beak and feather disease virus and pigeon circovirus, and that FiCV and canary circovirus were the most closely related avian circoviruses. Pairwise comparisons showed that the capsid proteins of FiCV and GuCV shared highest amino acid identity values with those of canary circovirus (62.0%) and pigeon circovirus (40.6%), respectively. The 5' intergenic region of GuCV was longer (207 nucleotides) and contained more direct and inverse repeated sequences than those of other circoviruses, while the 3' intergenic region of FiCV was notable in being longer (307 nucleotides) than its counterparts in other circoviruses and in containing two long repeats of 77 nucleotides.