Mitochondrial heteroplasmy is the existence of two or more mitogenomes within a single individual. Generally, it is considered to be a rare, transient condition in natural populations that arises due to spontaneous mutations in mitochondrial DNA. However, using Sanger sequencing, cloning and NGS we have identified widespread heteroplasmy in an Australian hylaeine bee, Amphylaeus morosus. Not only was every sequenced individual heteroplasmic from its southern-most to northern-most latitudinal limit (Victoria to southern Queensland), but every individual possessed the same two mitochondrial haplotypes, with no variation between individuals despite the large range of this species. A consistent, double infection of the reproductive parasite Wolbachia was also identified in these bees. Wolbachia has recently been receiving a lot of attention for its ability to affect sex-determination of its hosts and how this mechanism can be harnessed in the application of a bio-control agent. We discuss the possibility that the two conditions in A. morosus, mitochondrial heteroplasmy and a double Wolbachia infection, are not coincidental in this species, and whether mitochondria heteroplasmy may be driven by the persistent double infection. Hylaeinae is a highly diverse sub-family of bees that have extraordinary rates of species radiation within Australia and throughout the world. We suggest that this genus may be a good candidate for examining the role of Wolbachia in speciation and also the maintenance of intra-specific mitochondrial diversity.