The coconut rhinoceros beetle, Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures. Using larvae collected from Taiwan, we present a 16S metagenomic assay to understand the microbiome of different sections of the insect’s digestive tract, and a de novo transcriptomics assay of the fat body, gastric cecae, midgut, and hindgut.