This study measured the changes of microorganisms in the midgut and habitat niche ofRhynchophorus ferrugineusOlivier, an invasive quarantine pest, by Illumina sequencing. The bacterial diversity in theR. ferrugineuslarvae midgut and their habitat niche was compared to the uninfectedP. sylvestris. The Proteobacteria and Firmicutes occupied a dominant position in theR. ferrugineusmidgut and infectedP. sylvestris, while in the uninfectedP. sylvestristhe predominant bacterial phylum was the Cyanobacteria.Enterobacter,Dysgonomonas, andEntomoplasmawere the dominant bacterial genera inR. ferrugineusmidgut and also within the infected trees and uninfected trees with low relative abundance. These bacteria could be exploited as the biopesticide vector to controlR. ferrugineuspopulation. Besides,Sphingobacterium,Shinella, andRhodobactergenera had the same distribution pattern in the infected and uninfectedP. sylvestris, and these bacteria were not found in the midgut ofR. ferrugineus. Interestingly,PaludibacterandParabacteroideswere only distributed in the wood fiber of the infectedP. sylvestris, which could be used as potential microbial markers to detect if the palm plants are damaged by theR. ferrugineus. The results of this study will be beneficial to the development of control strategies forR. ferrugineus.