The tomato leafminer, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), is a highly destructive insect pest in Solanaceae, particularly in tomato crops. In this study, bacteria symbionts of eggs, the whole body, and different tissues of the fourth instar larvae of two populations, Rasht and Karaj, were isolated and identified. Using the 16S rRNA procedure, all symbiont bacteria, whether cultured or non-cultured, were classified at the phylum level as Proteobacteria and Firmicutes. BLASTn analyses revealed an overlap of Wolbachia, Enterobacter, Pseudomonas, Staphylococcus, and Acinetobacter genera in both populations. However, Bacillus subtilis, and Serratia marcescens were found only in Rasht, while Paenibacillus sp. and P. pasadenensis were identified solely in the Karaj population. Phylogenetic analysis of all bacterial sequences, except Wolbachia, revealed a distant evolutionary relationship between the leafminer's symbionts and those of other lepidopterans. Thus, we could demonstrate the microbiota diversity of this insect pest across different locations. Furthermore, this research will provide insights for discovering new biorational control methods for T. absoluta based on the parasitic or mutualist symbionts.