Diaphorina citri is a vector of ‘Candidatus Liberibacter asiaticus,’ (CLas), associated with Huanglongbing, (HLB, or citrus greening) disease in citrus. D. citri exhibit at least two color morphotypes, blue and non-blue. Blue morphs have a greater capacity for long-distance flight as compared to non-blue morphs, but little else is known about how color morphology influences vector characteristics. Much of my research was developed to test the hypothesis that blue and non-blue color morphs of D. citri have variation in their immune systems and that these immune systems differences lead to differences in interactions with the insect’s microbiota. I showed that the color morphology of the insect is derived from pigmented cells of the fat body. Non-blue morphs acquire a higher level of CLas in their bodies from infected trees as compared to blue morphs. I used shotgun proteomics to study molecular difference of two-color morphs. Higher abundance of immunity-associated proteins in blue morphs and lower mortality rate due to Beauveria bassiana infestation as compared to non-blue morphs supports our hypothesis. During evolution, D. citri has lost its immunity-related pathways and proteins, which has been thought to favor the development of endosymbiosis with microbial partners. D. citri harbors ‘Candidatus Profftella armatura’ (Profftella), an endosymbiont with a presumed defensive role in the insect’s biology. Profftella produces large quantities of diaphorin, an antimicrobial polyketide compound. While the diaphorin biosynthesis pathway inside of the bacteria is inferred from sequencing of the Profftella genome, I hypothesize that diaphorin biosynthesis requires the initial precursor molecules that are derived from the insect. I hypothesize that the precursor is S- methylmalonyl-CoA, which is synthesized by the D. citri enzyme propionyl CoA (PCC). To test this model, I used virus induced gene silencing to reduce the expression of the PCC gene, and silenced insects were subjected to diaphroin analysis using targeted mass spectrometry. PCC-silenced D. citri had lower amounts of diaphorin, providing support for S-methylmalonyl-CoA as the initial building block for diaphorin biosynthesis. Interestingly, PCC silencing resulted in slight increase of CLas titer in D. citri. These results show Profftella plays a crucial role in the biology of D. citri and its CLas vectoring capacity. To better understand how D. citri interacts with its microbial population at molecular level, I tested the hypothesis that small non- coding RNA (snRNA) may be used for inter-organism communication between D. citri and members of its microbial community. I sequenced the snRNA from CLas (–) and CLas (+) nymph and adult D. citri. I identified about 80 novel candidate miRNAs for D. citri that are differentially expressed as a function of CLas infection and during insect development. I predicted 13 tRNA-derived fragments (tRF) from Profftella which Lys-(ttt) tRF has ~600k reads in each library. Expression of Lys(ttt)_tRF_ACP_1is limited to bacteriome, where Profftella is housed. Lys(ttt)_tRF_ACP_1 localization through bacteriome shows its translocation after biosynthesis by Profftella which is localized at the center of bacteriome. In-silico target prediction with parallel transcriptome analysis showed that Lys(ttt)_tRF_ACP_1 may be involved in establishment of symbiosis and syncytial cell formation by Profftella. These data together will lead to better understanding of interactions between insects, insect vector-borne pathogens, and insect endosymbionts. Given the extraordinary conservation of endosymbiotic relationships across a range of insect vector taxa, including insect vectors of plant and animal pathogens, the molecular pathways regulating these interactions are a promising point for the development of novel and biologically based disease control strategies.