Abstract: Monitoring Editor: Kerry S. Bloom Replication-associated recombinational repair is important for genome duplication and cell survival under DNA damage conditions. Several nonclassical recombination factors have been implicated in this process, but their functional relationships are not clear. Here, we show that three of these factors, Mph1, Mms2 and the Shu complex, can act independently to promote the formation of recombination intermediates during impaired replication. However, their functions become detrimental when cells lack the Smc5/6 complex or Esc2. We show that mph1Delta, mms2Delta and shu1Delta suppress the sensitivity to the replication blocking agent MMS in smc6 mutants, with double deletions conferring stronger suppression. These deletion mutations also rescue the MMS sensitivity of esc2Delta cells. In addition, 2D gel analysis demonstrates that mph1Delta, mms2Delta and shu1Delta each reduce the level of recombination intermediates in an smc6 mutant when cells replicate in the presence of MMS, and that double deletions lead to a greater reduction. Our work thus suggests that Mph1, Mms2 and the Shu complex can function in distinct pathways in replication-associated recombinational repair, and that the Smc5/6 complex and Esc2 prevent the accumulation of toxic recombination intermediates generated in these processes.