The role of bacterial endosymbionts in insects has been associated with several physiological processes, including digestion. Development of new molecular tools has allowed the discovery of microorganisms that manipulate insect reproduction, development and even provide defense against parasitoids and pathogens. In this study we investigated the presence of bacteria inside the red imported fire ant (Solenopsis invicta) midgut using two different methods. First, we captured images using Transmission Electron Microscopy (TEM) and second, we isolated and cultured the microorganisms for molecular analysis. The small-subunit ribosomal RNA gene was amplified from bacterial genomic DNA using the Polymerase Chain Reaction (PCR) and consensus sequence primers. Restriction Fragment Length Polymorphism (RFLP) analysis revealed ten unique profiles. These isolates were identified to at least the genus level when queried against the NCBI database. Three of the strains were genetically modified with the plasmid vector pZeoDsRed and successfully reintroduced into fire ant colonies. Strong fluorescence of DsRed was detected throughout the larval stage (up to seven days after introduction). The transformed bacteria can still be rescued after pupal emergence; however most were passed out in the meconium. We further demonstrated that nurses contributed to the spread of the engineered bacteria within the colony by feeding the meconium to naive larvae. The role of these bacteria is being investigated by measuring the effects on the larvae and colony following antibiotic treatment. Molecular tools are also being used to determine the abundance and diversity of bacteria in samples from different counties and states.