Homologous recombination is a complex process that has several important roles: repair of broken DNA, repair of disintegrated replication forks and generation of genetic diversity. Two independent recombination pathways, RecBCD and RecF(OR), operate in Escherichia coli. Both pathways are involved in the initial stages of recombination i.e. in preparation of 3' terminated single stranded (ss) DNA covered with RecA protein, a RecA-ssDNA filament. RecBCD and RecF pathway use different enzymes to make this intermediate, but the enzymatic activities are similar: helicase activity to unwind DNA, a nuclease activity to degrade 5' strand leaving a 3' ssDNA and RecA loading activity to cover ssDNA with RecA. In the next step of recombination pathways, synapsis, RecA mediates homologous pairing, strand invasion and formation of a Holliday junction. In the postsynapsis, branch migration by RuvAB or RecG helicases extend heteroduplex intermediate and the final recombination products are generated by resolution of heteroduplexes by RuvC nuclease which is a part of a complex with RuvAB. RecA and single strand binding (SSB) proteins that promote homologous DNA pairing and the RuvABC complex or RecG that resolves Holliday junctions are shared by both recombination pathways. Even though both pathways function in the first steps of homologous recombination, presynapsis, they act on different DNA substrates. The recombination involving linear DNA with double-strand DNA ends and dsDNA break (DSB) repair in wild-type E. coli proceeds by the RecBCD pathway. The RecF pathway mediates recombination at single-strand gaps (SSG) and on circular DNA substrates. These two recombination pathways are equally important and both participate in DNA damage repair during normal growth. The third RecE pathway operates only in some strains of E. coli K12 that carry a silent, lambda-like prophage and only if those cells acquire a mutation that activates transcription of the prophage recombination genes.