Wolbachia

Last week I got dazzled!
The bacteria Wolbachia alters the mtDNA of the host so that two (or more) different species within the same genera has exactly same mtDNA sequences. In my case they are so closely related that the species I look at have also identical 28S D2 sequences. So how can I know that they are the same species or not. Morphology tells they are not same... I'll have to sequence ITS2...