Checkpoint responses change as cells proceed through the cell cycle. Here we describe a novel checkpoint gene in fission yeast, mrc1 (mediator of replication checkpoint), that confers activation of the checkpoint kinase Cds1 to DNA synthesis (S) phase. Mrc1 associates with Cds1 and is required for regulation of Cds1 by the checkpoint kinase Rad3. Mrc1 is regulated by the cell cycle, with the appearance of Mrc1 mRNA and protein coinciding with S phase. We propose that coordinated expression of Mrc1 with replication control proteins helps to ensure activation of the appropriate checkpoint response during DNA replication.