The processing of the Holliday junction by various proteins is a major event in DNA homologous recombination and is crucial to the maintenance of genome stability and biological diversity. The proteins RuvA, RuvB and RuvC play central roles in the late stage of recombination in prokaryotes. Recent atomic views of these proteins, including protein-protein and protein-junction DNA complexes, provide new insights into branch migration mechanisms: RuvA is likely to be responsible for base-pair rearrangements, whereas RuvB, classified as a member of the AAA(+) family, functions as a pump to pull DNA duplex arms without segmental unwinding. The mechanism of junction resolution by RuvC in the RuvABC resolvasome remains to be elucidated.