Feline immunodeficiency virus (FIV) infection is a retroviral infectious disease of domestic cats and is one of the leading causes of death of infectious etiology among cats. The disease is spread among the population of domestic cats around the world with high prevalence in urban areas. As other members of the genus Lentivirus, FIV causes persistent infection by transcribing viral ribonucleic acid (RNK) into proviral deoxyribonucleic acid (DNA) and incorporating it into the host genome. Because of its similarity with the human immunodeficiency virus (HIV), FIV presents a valuable research model for finding more effective treatment and HIV immunoprophylaxis. Given that etiologic treatment of the infected individual is not possible to carry out and that the immunoprophylaxis does not protect the cats from the phylogenetically different subtypes of field viral strains, general prophylactic measures represent the most significant model for prevention and suppression of the infection. Knowledge of the phylogenetic characteristics of field viral strains is one of the prerequisites for the development of more effective diagnostic and immunoprophylactic measures. The aim of this study was to determine the persistent infection from the feline immunodeficiency virus by proving the specific nucleotide sequences of the provirus env gene. The persistent infection was first proved in the Republic of Croatia in 14 FIV serologically positive cats by the stated molecular method. Phylogenetic analyses of the multiplicated sequence of FIV proviral env gene, along in comparison with the sequences of env gene from the gene bank, identified the phylogenetic affiliation of all 14 isolates from the territory of the Republic of Croatia to the viral subtype B. In addition to belonging to the viral B subtype, the isolates are phylogenetically shown to correlate with the other isolates from the nearest geographic region. Most of the nucleotide sequences obtained by this research show the most resemblance with the isolates of the feline immunodeficiency virus from Austria. Although phylogenetically all 14 nucleotide sequences of the proviral env gene belong to the B subtype, their mutual heterogeneity is also observed.