Major insect lineages have independently acquired bacterial species, mainly from Gamma-proteobacteria and Bacteroidetes class, which could be nutritional mutualistic factories, facultative mutualists that protect against biotic and abiotic stresses, or reproductive manipulators (which alter the fertility of the host species in its benefit). Some of them are enclosed in bacteriocytes to assure their maternal transmission over generations. All of them show an increased level of genetic drift due to the small population size and the continuous population bottlenecking at each generation, processes that have shaped their genome, proteome, and morphology. Depending on the nature of the relationship, the degree of genome plasticity varies, i.e., obligate nutritional mutualistic symbionts have extremely small genomes lacking mobile elements, bacteriophages, or recombination machinery. Under these conditions, endosymbionts face high mutational pressures that may drive to extinction or symbiont replacement. How do then they survive for such long evolutionary time, and why do they show a genome stasis? In this chapter, after a brief introduction to the problem, we will focus on the genome changes suffered by these endosymbionts, and on the mutational robustness mechanisms, including the moonlighting chaperone GroEL that could explain their long prevalence from an evolutionary perspective by comparing them with free-living bacteria.