The long-established view of Wolbachia as reproductive parasites of insects is becoming complicated as an increasing number of papers describe a richer picture of Wolbachia-mediated phenotypes in insects. The search for the molecular basis for this phenotypic variability has been greatly aided by the recent sequencing of several Wolbachia genomes. These studies have revealed putative genes and pathways that are likely to be involved in the host-symbiont interaction. Whereas significant progress is being made from comparative genomic studies together with the use of model host systems like Drosophila, the ultimate linking of phenotype to genotype will require the development of genetic manipulation technology for both host and symbiont.