Three primary species from theBegomovirusgenus,Pepper yellow leaf curl Indonesia virus(PepYLCIV),Tomato yellow leaf curl Kanchanaburi virus(TYLCKaV), andTomato leaf curl New Delhi virus(ToLCNDV), are suspected of spreading throughout pepper production centers, and plants are infected by a single species or a combination of two or three species. This study was conducted to provide complete information about the symptoms, incidence and severity, whitefly biotypes, as well as the dominance status of the threeBegomovirusspecies in pepper-producing areas in Java. A DNA analysis was carried out on leaf samples to identifyBegomovirusspecies and biotypes ofB. tabacicollected from 18 areas (16 districts) in lowlands (<400 m asl) and highlands (>700 m asl). The DNA analysis showed thatB. tabacibiotype B was the most commonly detected in all locations compared to the A, AN, and Q biotypes. The incidence of begomovirus infection was at a high level, 93% and 88.78% in the lowlands and highlands, respectively. However, the severity of begomovirus infection was significantly higher in the lowlands (54.50%) than in the highlands (38.11%). A single infection of PepYLCIV was most dominant in all locations sampled and caused severe infection, followed by a mixed infection with TYLCKaV. Therefore, the current status of begomovirus infection, especially PepYLCIV, can provide advice to farmers using more tolerant and resistant varieties as well as a breeding strategy for resistant pepper varieties.