Stable infections by maternally transmitted symbionts are frequently found in field populations, especially in arthropods. Many questions remain regarding their contribution to host biology and ecology, and especially on environmental adaptation of their host. Wolbachia is one of the most common endosymbiont of invertebrates. This cytoplasmically inherited endocellular bacterium induces number of reproductive alterations in its arthropod hosts and various fitness effects that allow it to spread in host populations. To better understand the influence of Wolbachia on host phenotypes and consequences of the manipulation of reproduction on the host genetic differentiation, it is crucial to be able to discriminate Wolbachia strains and determine their prevalence, which requires exhaustive screening. In the present report, we proposed the use of a new tool for the population studies, based on the high resolution melting (HRM) analysis, less expensive and faster than the ‘classical’ methods for large-scale studies. We investigated the effectiveness of HRM to explore and characterize the diversity of Wolbachia strains. Results obtained showed that HRM is a powerful tool to identify strains and detect polymorphism in singly infected hosts. When individuals harboured a mixture of Wolbachia strains (multiple infections), there is a risk of underestimation of the diversity if the proportions of the strains are highly different. However, the same limitations exist for the other techniques commonly used. Overall, this study demonstrated that HRM analysis is a rapid and reliable technique useful for studying, without a priori, Wolbachia strains diversity in field populations.