The α-proteobacterium Wolbachia pipientis is a very common cytoplasmic symbiont of insects, crustaceans, mites and filarial nematodes. To enhance its transmission, Wolbachia has evolved a large scale of host manipulations: parthenogenesis induction, feminization and male killing. Wolbachia’ s most common effect is a crossing incompatibility between infected males and uninfected females termed Cytoplasmic Incompatibility (CI). Little is known about the genetics and biochemistry of these symbionts because of their fastidious requirements. Such inherited microorganisms are thought to have been major factors for the evolution of sex determination and speciation. Wolbachia isolates are also of interest as vectors for the modification of wild insect populations and biological pest control. The means by which Wolbachia induces CI are currently unknown. However, there is a general consensus that Wolbachia somehow modifies sperm during spermatogenesis and this modification has to be rescued by the same bacterial strain in the egg, for normal development to proceed. In any other case, paternal chromosomes behave abnormally after fertilization and the embryo dies due to asynchronous mitoses. This thesis approached the mechanism of CI by different aspects. Firstly, in preparation for complete genome sequencing project, I estimated the genome sizes of two Wolbachia strains using pulse-field gel electrophoresis and developed a method to purify Wolbachia chromosomal DNA. Secondly, I demonstrated that Wolbachia infections could be simply established, maintained and stored in vitro using standard tissue culture techniques. Finally and most importantly, I monitored the bacterium during germ line development of the fly, where Wolbachia exerts its action. Particularly, I described the growth and distribution of Wolbachia during spermatogenesis, oogenesis and embryogenesis in several different host/symbiont genetic combinations in Drosophila species. Considerable intra- and inter-strain variation in Wolbachia density and tissue distribution was observed. To dissect the relative contribution of host and symbiont factors to the expression of CI I compared the properties of a single Wolbachia strain in different host genetic backgrounds and different Wolbachia strains in the same host background. These experiments demonstrated that the ability to express CI is an intrinsic Wolbachia trait and is not determined by host factors. The level of sperm modification in those lines harboring bacteria capable of modifying sperm however is influenced by host genetic background. Finally, numbers of infected sperm cysts are positively correlated with CI levels. From an evolutionary point of view, it seems that host-symbiont co-evolution is leading to low CI levels, high maternal transmission and low fitness cost of the infection. These three factors are probably linked through a unique feature: bacterial density. Ultimately, a complete understanding of CI will include unraveling the deeper relationships between developmental dynamics of infection and the interplay of host genetic backgrounds with Wolbachia.