The horn fly Haematobia irritans (Linnaeus, 1758) (Diptera: Muscidae) is one of the most important ectoparasites of cattle. The parasitism of horn flies interferes with cattle feeding, thus reducing weight gain and milk production. Additionally, horn flies are mechanical vectors of pathogens that cause disease in cattle. The aims of this study were to identify microorganisms in partially fed female horn flies through mining of expressed sequence tags (ESTs) and to characterize microorganism prevalence using real-time RT-PCR. Seven unigenes containing 24 ESTs were homologous to infectious agents. Microorganisms identified in partially fed female horn flies ESTs included Nora virus (3 unigenes; 8 ESTs), Wolbachia endosymbionts (3 unigenes; 3 ESTs), and Mycobacterium bovis (1 unigene; 13 ESTs). These results expanded the repertoire of microorganisms that could cause persistent infections or be mechanically transmitted by horn flies and support further studies on the role of horn flies in the epidemiology of these pathogens in Mexico.