(1) Background: (Hymenoptera: Eulophidae) is a global invasive pest that seriously damages eucalyptus plants and has caused serious harm to forestry production in many countries. Two genotypically distinct lineages of have been detected outside of Australia, namely, lineage A and lineage B. However, the composition and abundance of endosymbiotic bacteria in are still unclear between lineages. Therefore, the purpose of this study was to compare the bacterial communities in female adults of of different lineages distributed in the same domain; (2) Methods: The PacBio Sequel II platform was used to compare bacterial community composition between lineages of by sequencing the V1-V9 region of the 16S rRNA gene, and fluorescence quantitative PCR was used to compare the relative expression of between lineages of ; (3) Results: A total of 437 operational taxonomic units (OTUs) were obtained. These OTUs were subdivided into 20 phyla, 32 classes, 77 orders, 129 families, and 217 genera. At the genus level, the dominant bacteria in lineage A and lineage B were and , respectively. There were differences in the bacterial community of between lineages, and the abundance and relative expression of in lineage A were significantly higher than those in lineage B; (4) Conclusions: There were differences in the bacterial community of between lineages, and the abundance and relative expression of in lineage A were significantly higher than those in lineage B.