In fission yeast, maintenance of genome ploidy is controlled by at least two mechanisms. One operates through the Cdc2/Cdc13 kinase, which also involves the CDK inhibitor Rum1, and the other through the S-phase regulator Cdc18. By screening for sterile mutants that show increased ploidy, we have identified a new gene, pop1+, in mutants that become polyploid. The pop1 mutation shows a synthetic lethal interaction with the temperature-sensitive cdc2 or cdc13 mutation. In a pop1 mutant Rum1 and Cdc18 proteins become accumulated to high levels. The high ploidy phenotype in the pop1 mutant is dependent on the presence of the rum1+ gene, whereas the accumulation of Cdc18 is independent of Rum1. The predicted sequence of the Pop1 protein indicates that it belongs to a WD-repeat family with highest homology to budding yeast Cdc4, which participates in the ubiquitin-dependent pathway. Consistent with this notion, in a mutant of the 26S proteasome, higher molecular weight forms of Rum1 and Cdc18 are accumulated corresponding to polyubiquitination of these proteins. In the pop1 mutant, however, no ubiquitinated forms of these proteins are detected. Finally we show that Pop1 binds Cdc18 in vivo. We propose that Pop1 functions as a recognition factor for Rum1 and Cdc18, which are subsequently ubiquitinated and targeted to the 26S proteasome for degradation.