To determine the prevalent subtypes of feline immunodeficiency virus (FIV) in the domestic cat population in Taiwan during 2005-2006, the variable V3-V5 region of the envelope (env) gene was amplified by a nested PCR from the samples of whole blood of 18 FIV antibody positive cats. The blood samples were collected from animals in the animal shelters and from clinical cases in the Veterinary Hospital at National Taiwan University. Within the 18 serum positive samples, 12 samples were successful amplified by PCR. After sequencing and phylogenetic analysis of PCR products, 11 samples were clustered within group of subtype C, which is consistent with previous reports. However, the remaining one sample was grouped within subtype B; this is the first time this subtype has been identified in Taiwan. This observation suggests the need of a more comprehensive epidemiological survey before appropriately evaluation of the use of FIV vaccine in Taiwan.