All aspects of hosts’ life are affected not only by symbiotic bacterial community but also endosymbionts, such as physiological function, mating preference and fitness. Wolbachia, one of the most common endosymbionts, known as a manipulator of host sex ratio, may also have a huge effects on other symbionts. Here, we assessed the effects of Wolbachia on the diversity and structure of other symbiotic microbial communities in six ant species by using next-generation sequencing. Our results show that the diversity of the symbiotic microbial communities between Wolbachia-positive species and negative species is not different. However, according to the Wolbachia infection, dominant symbiotic microbes of each host species were different as well as the composition of the overall symbiotic microbial community. Thus, this study suggests that, as Wolbachia have an important role in shaping microbiome of hosts, endosymbiont infection status deserves special consideration in studying microbiome.