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TAS-ELISA detection samples which was infected banana bunchy top virus (BBTV), cloning two genome of BBTV HaiKou 2 and BBTV HaiKou 4 isolates of its total DNA template of tender pseudostem and leaf by Reverse-PCR method. The result shows, the full-long sequence of HaiKou 2 DNA 1-6, Satellite DNA are 1103, 1067, 1058, 1041, 1013, 1082 and 1093 nt, respectively, HaiKou 4 DNA1-6 full-long sequence as 1103, 1055, 1059, 1041, 1013 and 1081 nt, respectively. Each component of two isolates non-coding region including one high homologous CR-SL and CR-M; Coding region has a open reading frame (ORF), and a small ORF existence inside DNA1 large ORF. Sequence analysis shows, DNA1 component of two isolates comparing of others are the most conservative. DNA2 component are maximum variation. According to Karan classification, we show that HaiKou 2 and HaiKou 4 isolates are the member of Asian group. In addition, HaiKou 2 isolate exists Satellite DNA, coding one of 33.1kD replication initiation protein, while HaiKou 4 isolate was does not existence.