The widespread intracellular bacterium Wolbachia is transmitted exclusively maternally and alters the reproduction of its hosts by different mechanisms. Thereby, inheritance patterns of mitochondrial genomes are modified, possibly confining interpretations of mitochondrial sequence data. Although this phenomenon has been reported before, its conclusions seem to be widely ignored. In the light of recent large-scale barcoding projects relying solely on mitochondrial cox1 sequences, we screened the native German bee fauna (Anthophila) for Wolbachia infections. The screening revealed that 66% of the native German bees and 54% of sphecid wasps are infected by Wolbachia. Many species bore identical or similar infections, suggesting a high rate of horizontal transfer. Supergroup A infections were recovered in most cases; only one species bore a super-group F Wolbachia infection. Because Wolbachia is not only present in 66% of bees but also in the majority of arthropod species, we argue that studies interpreting sequence data of arthropod species cannot rely on mitochondrial data alone – nuclear markers must be incorporated. DNA barcoding using only mitochondrial cox1 will not be sufficient to delimit, identify or discover Wolbachia-infected species, i.e. probably the majority of all animal species.