The spread of photosynthesis is one of the most important but controversial topics in eukaryotic evolution. Because of massive gene transfer from plastids to the nucleus and because of the possibility that plastids have been lost in evolution, algal genes in aplastidic organisms often are interpreted as footprints of photosynthetic ancestors. These putative plastid losses, in turn, have been cited as support for scenarios involving the spread of plastids in broadscale eukaryotic evolution. Phylogenomic analyses identified more than 100 genes of possible algal origin in Monosiga, a unicellular species from choanoflagellates, a group considered to be the closest protozoan relatives of animals and to be primitively heterotrophic. The vast majority of these algal genes appear to be derived from haptophytes, diatoms, or green plants. Furthermore, more than 25% of these algal genes are ultimately of prokaryotic origin and were spread secondarily to Monosiga. Our results show that the presence of algal genes may be expected in many phagotrophs or taxa of phagotrophic ancestry and therefore does not necessarily represent evidence of plastid losses. The ultimate prokaryotic origin of some algal genes and their simultaneous presence in both primary and secondary photosynthetic eukaryotes either suggest recurrent gene transfer events under specific environments or support a more ancient origin of primary plastids.