[Objective] In order to understand the relationship between endophytic bacterial diversity of banana and fusarium wilt disease, thus providing a scientific basis for the biological control against fusarium wilt. [Methods] Endophytic bacterial diversity and communities of different plant tissues of two banana cultivars with different resistance to fusarium wilt were examined using Terminal Restriction Fragment Length Polymorphism (T-RFLP). [Results] The results indicated that resistant cultivar “Nongke No.1” showed more abundant endophytic bacterial diversity than that of susceptible cultivar “Brazil” in the root, pseudomeristem and leaves of plants. Diseased plants conserved more abundant endophytic bacterial diversity than that of healthy plants in different tissues. Endophytic bacterial diversity of “Nongke No.1” kept basically stabilized, but that of “Brazil” showed a great range of variation among healthy and different diseased stages. Dominant bacterial populations were various in the different tissues, and there were some specific dominant populations in the healthy and diseased banana plants of different cultivars. [Conclusion] The results indicated that resistant cultivar showed more abundant and steady endophytic bacterial diversity than that of susceptible cultivar. Diseased plants showed more abundant endophytic bacterial diversity than healthy plants. In addition, there is a marked diversity of dominant populations in different plants between resistant or susceptible cultivars to fusarium wilt disease.