CDK8 and CDK19 form a highly conserved cyclin-dependent kinase subfamily that binds to and inhibits the essential transcription complex, Mediator, and is thought to also activate gene expression by phosphorylating the C-terminal domain (CTD) of RNA polymerase II. Cells lacking either CDK8 or CDK19 are viable and have somewhat limited transcriptional alterations, but how they regulate expression of different genes has not been explained, and whether one of the two kinases must be expressed to allow cell differentiation is unknown. Here, we find that CDK8 and CDK19 are largely functionally redundant for tissue-specific gene expression. Genetic deletion of CDK8 in mice does not affect normal intestinal homeostasis and efficient tumourigenesis, and CDK8 is not required in vivo in cells lacking the main PolII CTD kinase, CDK7. Individual knockout of genes encoding CDK8 or CDK19 in intestinal organoids has only limited effects on gene expression due to their extensive functional redundancy in control of gene expression. Surprisingly, although their combined deletion in organoids reduces longterm proliferative capacity, it is not lethal and allows differentiation. Nevertheless, either CDK8 or CDK19 is required to maintain expression of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) pathway. In double mutant organoids, the CFTR pathway is downregulated, leading to mucus accumulation and increased secretion by goblet cells. Pharmacological inhibition indicates that expression and function of the CFTR pathway is dependent on CDK8/19 kinase activity. We conclude that expression of the Mediator kinases is not essential for cell proliferation and differentiation, but they cooperate to regulate tissuespecific transcriptional programmes.