The Kin28 protein kinase interacts physically and genetically with cyclin Ccl1. Kin28 has been reported recently to be involved in the in vivo phosphorylation of the largest subunit of RNA polymerase II (Rpb1) in Saccharomyces cerevisiae. Now, we show that in a strain harboring a conditional ccl1-ts mutation, the C-terminal domain (CTD) of the Rpb1 subunit is under-phosphorylated at restrictive temperature. The transcription of a set of genes, chosen at random, is severely affected in a kin28-ts mutant shifted at restrictive temperature. Here, we report that the same set of genes requires a functional CCL1 gene product to be transcribed. These findings, added to previously published data, establishes that Kin28p is a cyclin-dependent kinase (CDK) with Ccl1p as a companion, both of them being necessary for general transcription and CTD phosphorylation.