Polyomavirus infections were detected in 40 companion bird individuals belonging to a broad species range of estrildid and fringillid finches and originating from 21 different bird aviaries. Based on partial virus protein 1 (VP1) sequences, the viruses were identified as Serinus canaria polyomavirus 1 and Pyrrhula pyrrhula polyomavirus 1. Serinus canaria polyomavirus 1 was found in 18 birds belonging to one estrildid and four fringillid species. Pyrrhula pyrrhula polyomavirus 1 was detected in 22 birds of six estrildid and three fringillid species. There was a large overlap in host range. Increased mortality was frequently found in the affected bird aviaries while clinical signs were diverse. Co-infections with other viruses, bacteria or fungal pathogens were common and might have influenced the clinical signs. Sequence analyses, including partial VP1 sequences of the 40 virus strains, and full genome sequences of selected strains revealed a high genetic heterogeneity among virus subgroups of Serinus canaria polyomavirus 1 and Pyrrhula pyrrhula polyomavirus 1, indicating the existence of two virus variants for both virus species. For Pyrrhula pyrrhula polyomavirus 1, two genotypes were found that associated with the family of the finches, Estrildidae or Fringillidae.