Eukaryotic algae obtained the capacity to carry out oxygenic photosynthesis through endosymbiosis with a cyanobacterium that evolved to become the chloroplasts. These organelles still have a remnant bacterial genome encoding photosystems and several other functions. In addition, eukaryotic algae live in close association with a wide diversity of bacteria whose functions and genomes are not well understood. Some recent work from my laboratory aims to fill in some of the gaps in our knowledge of the evolutionary dynamics of chloroplast genome evolution and bacterial symbiont associations, using a group of siphonous green algae as a model. In the low-light genus Ostreobium, we observe an evolutionary trend towards very small, densely packed chloroplast genomes with very low rates of genome rearrangement. Many lineages of bacteria are found as intracellular endosymbionts of siphonous green algae, some of which are shown to be predominantly affected by environmental factors while others are strongly determined by host relationships. Through holobiont genome sequencing, we are currently characterising the potential nature of metabolic hand-offs and the genome dynamics of these intracellular interactions.