Tephritid pests, such as the Mexican fruit fly, Anastrepha ludens (Loew), represent a major threat to fruit production worldwide. In order to control these pests, sterile insect technique is used to suppress and eradicate wild populations. For this control method to be successful, hundreds of millions of flies must be produced weekly in mass rearing facilities. The large quantity of artificial diet and close proximity of flies at various life stages allows bacteria from family Enterobacteriaceae, Bacillaceae, Pseudomonadaceae, and others to multiply and spread more easily. In this study, bacteria with a possible pathogenic effect were isolated from Mexican fruit fly eggs and dead Mexican fruit fly larvae. Two strains of bacteria associated with dead and dying larvae were identified using the 16S rRNA sequence as a species of Morganella. Further sequencing of multiple genes and the entire genomes identified both strains as Morganella morganii. Pathogenicity tests were completed to assess this bacterium as a Mexican fruit fly pathogen. Several measures of pathogenicity including effects on larval and pupal weight, adult percent emergence, and flight ability were measured for the 2 strains of Morganella compared against a control. In all cases, the presence of the Morganella strains significantly reduced all quality control measurements compared to the control. Also, at 105 colony forming units per ml or higher levels of inoculum, the presence of Morganella resulted in 100% mortality of larvae. This study illustrates that Morganella morganii is an extremely lethal pathogen of mass reared Mexican fruit flies.