Abstract: Indonesia possess one of the largest genetic diversities of banana in the world, both cultivated and wild. However, the number of disease especially Fusarium wilt has reduce the production of banana. Parthenocarpy, polyploidy and sterility has also become a problem for the development of new varieties that resistant to the diseases. One of the largest plant R-gene families encodes a protein with Nucleotide Binding Site (NBS) domain. The aim of this study was to identify the candidate gene of NBS from Musa acuminata var. malaccensis and Musa acuminata cv Cavendish. In this study, two fragments (P 5-8 and P 5-10) of NBS type gene from Musa acuminata var. malaccensis and one fragment (P 5-11) from Cavendish were amplified with degenerate primer, cloned and sequenced. Amino acid sequences revealed 97-100% similarity with RPM1 (P 5-10 and P 5-11) and RPS2 (P 5-8) from Musa acuminata var. malaccensis. Contig sequences were deposited in Genbank and assigned number KP 691062 -KP691064. There were four conserved motif sequences i.e., P-loop, kinase-2, kinase-3a and hydrophobic domain. All of the fragments was grouped into non-TIR-NBS-LRR and contained in chromosome number 9. The conserved sequences of NBS gene can be used as a potential genetic marker for disease resistant gene in banana.