The coconut rhinoceros beetle (CRB), Oryctes rhinoceros, is a pest of palm trees in the Pacific. Recently, a remarkable degree of palm damage reported in Guam, Hawaii, Papua New Guinea and Solomon Islands has been associated with a particular haplotype (clade I), known as “CRB-G”, which can be distinguished by a molecular marker in the mitochondrial gene. In Palau Archipelago, it was reported that CRB-G and other haplotype (clade IV) belonging to the CRB-S cluster coexisted in the field. In this study, more than 75% of pheromone trap-captured adults of both of haplotypes were OrNV-positive by PCR. There was no significant difference in OrNV prevalence between the haplotypes. In tissues of PCR-positive CRB-G specimens from Palau, viral particles were observed by transmission electron microscopy. Hemocoel injection of CRB larvae with crude virus homogenates from these tissues resulted in viral infection and mortality. However, the OrNV isolates from Palauan beetles exhibited a lower level of viral production and longer larval survival times compared to OrNV isolate X2B, a typical isolate used for biological control of CRB in the Pacific. The full genome sequences of the Palauan and X2B isolates were determined and found to be closely related to each other. These results suggest that CRB adults in Palau are infected with a less virulent virus.