[Objectives]  To investigate the microbial composition of larvae and adults of the important stored grain pest Rhyzopertha dominica (Fabricius). [Methods]  The Illumina NovaSeq high-throughput sequencing platform was used to sequence the V3-V4 fragment of the bacterial 16S rDNA gene and the ITS1 fragment of the fungal ITS gene in larvae and adults of R. dominica. [Results]  Valid reads of 16S rDNA from larvae and adults were 256 551 and 249 101, which were clustered to 214 and 251 OTUs, respectively. Valid ITS reads from larvae and adults were 196 246 and 109 184, which were clustered to 547 and 963 OTUs, respectively. The Flavobacteriales endosymbiont of R. dominica (FERD) was the dominant bacterial genus in R. dominica, comprising for 63.77% of the larval, and 88.28% of the adult, microbiome, respectively. Alternaria was the most abundant fungus, comprising for 44.62% of the larval, and 7.10% of the adult, microbiome, respectively. Alpha diversity analysis showed that there is a significant difference in the microbial diversity index of larvae and adults, but no significant difference in the richness index. Beta diversity analysis indicates that there is a significant difference between the larval and adult microbiome. [Conclusion]  There are significant differences between the microbiomes of larval and adult R. dominica. Larvae had higher bacterial diversity, but lower fungal diversity, than adults. This study lays a foundation for the development of novel control technologies for stored grain pests based on “inhibiting microorganisms to control pests”, and research on the environmental adaptability of symbionts in R. dominica.