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Abstract Background Various endosymbiotic bacteria, including Wolbachia of the Alphaproteobacteria, infect a wide range of insects and are capable of inducing reproductive abnormalities to their hosts such as cytoplasmic incompatibility (CI), parthenogenesis, feminization and male-killing. These extended phenotypes can be potentially exploited in enhancing environmentally friendly methods, such as the sterile insect technique (SIT), for controlling natural populations of agricultural pests. The goal of the present study is to investigate the presence of Wolbachia, Spiroplasma,Arsenophonus and Cardinium among Bactrocera,Dacus and Zeugodacus flies of Southeast Asian populations, and to genotype any detected Wolbachia strains. Results A specific 16S rRNA PCR assay was used to investigate the presence of reproductive parasites in natural populations of nine different tephritid species originating from three Asian countries, Bangladesh, China and India. Wolbachia infections were identified in Bactrocera dorsalis, B. correcta, B. scutellaris andB. zonata, with 12.2–42.9% occurrence, Entomoplasmatales in B. dorsalis, B. correcta, B. scutellaris, B. zonata,Zeugodacus cucurbitae and Z. tau (0.8–14.3%) and Cardinium in B. dorsalis andZ. tau (0.9–5.8%), while none of the species tested, harbored infections with Arsenophonus. Infected populations showed a medium (between 10 and 90%) or low (