Adeno-associated viral (AAV) vector is attracting significant interest for use in gene therapy for genetic diseases, because of its unique and advantageous characteristics, compared to other currently available viral vectors. Eight natural serotypes of AAV have been identified, of which AAV serotype 2 is the one best characterized and most widely used in current gene delivery studies. The application of AAV serotype 2 in hemophilia B gene therapy is a promising development in gene therapy for genetic diseases such as hemophilia. Preliminary studies have demonstrated relation and distinction of host, genome sequences, replication, tropism, packaging of recombinant virions and cross-reactivity of neutralizing antibodies among different serotypes of AAV. This review summarizes the progress of studies in AAV serotypes and pertinent applications in hemophilia B gene therapy. The latest progress in gene delivery of coagulant factor IX (for hemophilia B) using AAV serotype vectors is described in detail.