Mitochondria and chloroplasts are eukaryotic organelles that were acquired through endosymbiosis. In the case of the mitochondrion, a heterotrophic cell engulfed and retained an alpha-proteobacterium. The engulfed bacterium, or endosymbiont, underwent extensive cellular and genetic integration with its host, thereby becoming an organelle. Chloroplasts are derived from the engulfment and retention of a photosynthetic cyanobacterium that also experienced loss of cellular functions and genetic material. Although mitochondria and chloroplasts retain their own genomes, most of the proteins that function in these organelles are encoded by genes that were transferred to the nucleus in a process known as Endosymbiotic Gene Transfer (EGT). Chloroplasts in plants, green algae and red algae are known as primary plastids. Other photosynthetic organisms have secondary plastids that were acquired by engulfing and retaining a primary plastid-bearing alga. In the process, the nucleus of the engulfed alga underwent EGT (and presumably gene loss) to such an extent that it disappeared completely except in two lineages, cryptophytes and chlorarachniophytes, which retain a highly reduced and miniaturized form known as a nucleomorph. To understand the process of EGT and endosymbiosis in general, the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans were sequenced. In the case of G. theta its nucleomorph is of red algal origin while the nucleomorph of B. natans is derived from a green algal endosymbiont. Prior to the nuclear genome projects the genomes of the three organelles – plastid, mitochondrion, nucleomorph – had already been sequenced. This allowed investigation of recent transfers of organellar DNA to the nucleus. Mitochondrial transfers to the nucleus are still occurring in both organisms but transfers of plastid and nucleomorph DNA are not. The nucleomorph genomes of B. natans and G. theta appear ‘frozen’, unable to undergo EGT and thus unable to disappear as they have in all other lineages with secondary plastids. The creation of a spliceosomal intron from transferred organellar DNA was investigated. I also investigated nuclear genes whose encoded proteins appear to function in the mitochondrion. 833 putatively mitochondrial targeted proteins were identified in G. theta and 720 in B. natans.