Abstract Wolbachia is a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects. Wolbachia can also be pathogenic, as is the case with w MelPop, a virulent variant of the endosymbiont of Drosophila melanogaster . An extensive genomic amplification of the 20kb region encompassing eight Wolbachia genes, called Octomom, is responsible for w MelPop virulence. The Octomom copy number in w MelPop can be highly variable between individual D. melanogaster flies, even when comparing siblings arising from a single female. Moreover, Octomom copy number can change rapidly between generations. These data suggest an intra-host variability in Octomom copy number between Wolbachia cells. Since w MelPop Wolbachia with different Octomom copy numbers grow at different rates, we hypothesized that selection could act on this intra-host variability. Here we tested if total Octomom copy number changes during the lifespan of individual Drosophila hosts, revealing selection for different Wolbachia populations. We performed a time course analysis of Octomom amplification in flies whose mothers were controlled for Octomom copy number. We show that despite the Octomom copy number being relatively stable it increases slightly throughout D. melanogaster adult life. This indicates that there is selection acting on the intra-host variation in the Octomom copy number over the lifespan of individual hosts. This within host selection for faster replicating bacterial symbionts may be in conflict with between host selection against highly pathogenic Wolbachia .