Mediator and RNA polymerase II (Pol II) form stable, condensate-like clusters in living stem cells, which are transcription-dependent. These clusters are colocalized and associate with chromatin, exhibiting properties of phase-separated condensates. The clusters merge rapidly, show rapid recovery in Fluorescence Recovery After Photobleaching (FRAP) assays, and are sensitive to transcriptional inhibitors. This suggests that Mediator and Pol II form condensates that may serve as a scaffold for transcriptional regulation, with Mediator clusters at enhancers transiently interacting with Pol II clusters at promoters.Mediator and RNA polymerase II (Pol II) form stable, condensate-like clusters in living stem cells, which are transcription-dependent. These clusters are colocalized and associate with chromatin, exhibiting properties of phase-separated condensates. The clusters merge rapidly, show rapid recovery in Fluorescence Recovery After Photobleaching (FRAP) assays, and are sensitive to transcriptional inhibitors. This suggests that Mediator and Pol II form condensates that may serve as a scaffold for transcriptional regulation, with Mediator clusters at enhancers transiently interacting with Pol II clusters at promoters.