Abstract: Pepper yellow leaf curl disease which is caused by Pepper Yellow Leaf Curl Virus (PepYLCV) is one of the major problems in chili pepper (Capsicum annuum) cultivation in Indonesia. Reducing of the yield could reach 100% in some condition. For this reason, well understanding of virus distribution as well as their genome structure is very crucial for combating the disease. Based on this rationality we characterized genome structure of PepYLCV isolate designated as PepYLCWSV-TD21 which was collected from chili cultivation pepper population in West Sumatera. The result indicated that the PepYLCWSV-TD21 had a monopartite genome and dominantly infected compared to its bipartite counterpart. This was confirmed by analysis of DNA-β presence by specific primer pair Beta01/Beta02. Annotation of both genome structure successfully identified 6 open reading frames designated as V1, V2, C1, C2, C3 and C4 in the DNA-A like genome, whereas only 1 open reading frame designated as C1 was identified in DNA-β. Further characteristics of each open reading frame were further elucidated. These results provided us information on distribution of monopartite PepYLCV in West Sumatera Indonesia, as well as its genome characteristic that in turn could be used as our start point for development of resistant chili pepper cultivar.