Modern views of eukaryote origins always entail endo-symbiosis, but the number and nature of endosymbiotic events is still debated. It is generally agreed among all theories that the mitochondrion arose from proteobacteria and that the plastid arose from cyanobactera. It is also agreed that those were singular and rare events in the history of life. The remaining debate concerns the origin of the host that acquired the mitochondrion and whether it was a prokaryote or a eukaryote and if the latter, whether additional endosymbio-ses were involved in its origin. Bioenergetic considerations indicate that the host that acquired the mitochondrion was a prokaryote, because the energy per gene that mitochondria provide was necessary to support the origin of the numerous evolutionary novelties that distinguish eukaryotes from prokaryotes. Yet other theories holding that the eukaryotic state arose before the acquisition of mitochondria remain popular. These include the notion that the nucleus arose as an endosymbiont or the view that eukaryotes are directly descended from planctomycetes. Theories for the origin of eukaryotes are, in principle, testable with genome data and inference tools of molecular phylogeny. Comparisons of genes present in the eukaryote common ancestor to genes in prokaryote genomes have uncovered evidence for the roles of an archaebacterium as the source of the genetic apparatus or informational genes, and a eubacterium as the source of energy metabolic functions, but for no other significant contributors. At the same time, the way in which microbial evolution, and lateral gene transfer (LGT) in particular, figure into endosymbiotic theory is gradually becoming apparent.