Avian polyomavirus is one of the most important viral pathogens of caged birds which every year results in significant economic losses for bird breeders and pet store owners. The most devastating disease outbreaks occur in large commercial aviaries of the budgerigar species where the birds are raised in large volieres with dozens or hundreds of free-flying birds. Both young and adult specimens of budgerigars are susceptible to infection. The mortality rate of hatchlings is often high and can approach 100% when the virus is first introduced into the aviary. The causative agent is a DNA virus from the family Polyomaviridae, genus Polyomavirus. The goal of this research is to determine the similarity of the investigated strains and compare them with the online available strains from international genome databases such as the NCBI database through phylogenetic analysis of the sequences of specifically amplified segments of the genome. In this research, we used archived samples from Department of Poultry Diseases with Clinic, previously isolated from the carcasses of pet birds. Total DNA was extracted from internal organs and amplified through PCR using specific primers. Afterwards, the amplified PCR products were sequenced using Sanger method to perform phylogenetic analysis. The phylogenetic analysis showed a certain degree of heterogeneity with respect to origin of the isolates, but not with respect to the bird species and breeder. According to the available literature, this was the first case where two phylogenetically distinct APV strains were isolated from two organs, liver and spleen, of the same host.