The acquisition of mitochondria and plastids via endosymbioses were central to the origin and diversification of eukaryotic life. However, since these evolutionary processes were initiated >1 billion years ago, the process of organellogenesis remains difficult to reconstruct. More recently acquired bacterial endosymbionts are found across eukaryotes. Some of these endosymbiotic associations show astonishingly high levels of symbiotic integration. We use the amoeba Paulinella chromatophora that contains nascent photosynthetic organelles of cyanobacterial origin and the trypanosomatid Angomonas deanei that contains b-proteobacterial endosymbionts to explore the molecular mechanisms underlying host-symbiont interaction and the transformation of bacterial endosymbionts into genetically integrated organelles.