In eukaryotes, it is unknown if mismatch repair (MMR) is temporally coupled to DNA replication and how strand-specific MMR is directed. Here we fused Saccharomyces cerevisiae MSH6 with cyclins to restrict the availability of the Msh2-Msh6 mismatch recognition complex to either S-phase or G2/M. The Msh6-S cyclin fusion was proficient for suppressing mutations at three loci that replicate at mid-S-phase, whereas the Msh6-G2/M cyclin fusion was defective. However, the Msh6-G2/M cyclin fusion was functional for MMR at a very late-replicating region of the genome. In contrast, the heteroduplex rejection function of MMR during recombination was partially functional during both S-phase and G2/M. These results indicate a temporal coupling of MMR, but not heteroduplex rejection, to DNA replication.