The outcome and the evolution of host-symbiont associations depend on environmental constraints, but responses are difficult to predict since they arise from a complex interaction between the host, the parasite and the environment. The situation can be even more complex when multiple parasite genotypes, with potentially different responses to environmental changes, coexist within a single host. In this paper, we investigated the effect of the temperature (from 14 to 26 °C) during the host development on the density of 3 strains of the intracellular bacterium Wolbachia that coexist within the wasp Leptopilina heterotoma. In this species, Wolbachia induces cytoplasmic incompatibility, a sperm-egg incompatibility that allows it to spread and persist in host populations. Using real-time quantitative PCR we found that (i) Wolbachia density is temperature-specific and highest at 26 °C; (ii) the order of the abundance of the 3 Wolbachia strains does not vary with temperature changes; (iii) the response of bacterial density to temperature occurs within a single insect generation, during the egg-to-adult developmental period; (iv) in this species, temperature-related changes in Wolbachia density do not influence cytoplasmic incompatibility.