PHO85 is a cyclin-dependent kinase (CDK) with roles in phosphate and glycogen metabolism and cell cycle progression. As a CDK, Pho85 is activated by association with Pho85 cyclins (Pcls), of which 10 are known. PCL1, PCL2 and PCL9 are the only members of the Pho85 cyclin family that are expressed in a cell cycle-regulated pattern. We found that PCL9 is expressed in late M/early G1 phase of the cell cycle and is activated by the transcription factor, Swi5. This pattern of regulation is different from PCL1 and PCL2, which are expressed later in G1 phase and are regulated primarily by the transcription factor SBF. Co-immunoprecipitation experiments using in vitro translated proteins showed that Pcl9 and Pho85 form a complex. Furthermore, immunoprecipitated Pcl9 complexes from yeast lysates were capable of phosphorylating the exogenous substrate Pho4. The Pcl9-associated kinase activity was dependent on PHO85, showing that Pcl9 and Pho85 form a functionally active kinase complex in vivo. Deletion of PCL9 in diploid cells caused random, rather than bipolar, budding in 18% of cells. In contrast, deletion of PCL2, the closest relative of PCL9, had no effect on the budding pattern. Deleting more members of the PCL1,2 subfamily (which includes PCL9) increased the percentage of random budding in the cell population. When all members of the PCL1,2 subfamily were deleted, 73% of cells budded randomly, a value similar to that obtained when the CDK partner PHO85 was deleted. Our results show that PCL9 and PHO85 form a functional kinase complex and suggest a role for Pho85 CDKs at the M/G1 boundary.