Wolbachia is perhaps the most ubiquitous symbiotic bacterium in the animal world. It is known to infect the majority of insect species, in which it induces a wide array of reproductive phenotypes. In Trichogramma, tiny parasitoid wasps often used for biological control of insect pests, Wolbachia converts the wasps to an asexual mode of reproduction through the induction of parthenogenesis. We do not have a thorough understanding of 1) the genetic and environmental factors that mediate the penetrance of the parthenogenesis phenotype, thus allowing Wolbachia to fix in a population, and 2) how the fixation of Wolbachia in a population affects genome evolution of the partners. In Chapters 1 and 2, I develop genomic resources for both the Wolbachia strain wTpre (Chapter 1), and its native host Trichogramma pretiosum (Chapter 2), and use comparative genomics to identify unique features of these genomes that could be implicated in the co-evolution of host and symbiont. In Chapters 3 and 4, I explore some of the genetic and environmental factors that affect the expression of wTpre’s parthenogenesis-inducing phenotype. In Chapter 3, I show that the rate of Trichogramma reproduction mediates the penetrance of the parthenogenesis phenotype. In Chapter 4, I look at the effects of outbreeding, and how the resulting combinations of new host-symbiont genotypes affect wTpre’s ability to induce parthenogenesis. By generating genomic resources for the system, and teasing apart the factors that determine the final host-symbiont phenotype, we can improve our understanding of how Wolbachia spreads and fixes in a population, and what the long-term consequences of fixation are for both symbiotic partners.