A key step in homologous recombination is the formation of a heteroduplex joint between double-stranded DNA and single-stranded DNA by the homologous pairing and strandexchange, and this step is also important in recombinational repair of damaged DNA in various organisms. The homologous pairing and the strand-exchange are promoted in vivo and in vitro by RecA protein of Escherichia coli or its homologues of bacteria, virus, and lower and higher eukaryotes. A central question on the mechanism of homologous recombination is how RecA protein (and its homologues) recognizes homologous sequences between single-stranded DNA and double-stranded DNA. Recent studies suggest that RecA protein promotes homologous recognition between these DNA molecules by the formation of a transient and additional pairing of identical sequences via non-Watson-Crick interactions to the Watson-Crick-type duplex DNA, and that RecA protein uses three non-equivalent DNA-strand-binding sites in this reaction.