The symbiosis relationship between arthropods and microorganisms is common in nature and may aid herbivores to counteract plant defences and increase fitness. The spider mite Tetranychus evansi is a pest of tomato that manipulates important defence pathways, including those that lead to the production of protease inhibitors, causing great economic impacts. This ability may be related to the action of endosymbionts present in this specie. Thus, this study aimed to identify the microbiota present in the two species of spider mites, Tetranychus evansi and Tetranychus urticae. Microbial DNA was extracted from mite samples and subjected to polymerase chain reaction denaturing-gradient gel electrophoresis (PCR-DGGE), and then submitted to sequencing. Fungi were not identified in any of the mites. The diversity of bacteria was greater in T. evansi. In both spider mites, most of the bacteria species belong to the Proteobacteria phylum. The greater diversity of bacteria found in T. evansi may be related to the ability of this mite to manipulate plant defences, and novel studies could focus on the role of each bacterium in this mechanism. The study of the diversity of microorganisms will help to understand their efficiency as agricultural pests and provide alternatives to combat them.