AbstractDivision of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic, oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation.In this proposal origin of eukaryots occur by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the genome of archaeal ancestor of eukaryots. Second, the double-strand break can be repaired intergenomically by complementary strands invasion. Third, this duplicated genome can be fissioned into two compartments by reciprocal genetic recombination. Scenario is accomplished by aberrant fission of the inner membrane surrounding separately those two compartments.