In living embryonic stem cells, Mediator and RNA polymerase II (Pol II) form transient and stable clusters that exhibit properties of phase-separated condensates. These clusters are transcription-dependent, colocalize with chromatin, and are sensitive to transcriptional inhibitors. Mediator clusters are recruited by transcription factors at large or clustered enhancer elements, and interact with large Pol II clusters in transcriptional condensates. The study used live cell super-resolution and light sheet imaging to directly observe the organization and dynamics of Mediator and Pol II. Mediator forms small transient clusters and large stable clusters, while Pol II also forms similar clusters. The stable clusters are colocalized and show dynamic behavior, including coalescence, rapid recovery in FRAP assays, and sensitivity to hexanediol. These findings suggest that Mediator and Pol II form in vivo condensates that may facilitate transcriptional regulation. The study also shows that Mediator clusters can dynamically interact with actively transcribing genes, supporting a dynamic kissing model where Mediator clusters occasionally colocalize with gene loci. The results imply that large Mediator clusters at enhancers can transiently interact with the transcription apparatus at promoters, influencing gene control mechanisms. The findings highlight the importance of spatial organization and dynamics in transcriptional regulation.In living embryonic stem cells, Mediator and RNA polymerase II (Pol II) form transient and stable clusters that exhibit properties of phase-separated condensates. These clusters are transcription-dependent, colocalize with chromatin, and are sensitive to transcriptional inhibitors. Mediator clusters are recruited by transcription factors at large or clustered enhancer elements, and interact with large Pol II clusters in transcriptional condensates. The study used live cell super-resolution and light sheet imaging to directly observe the organization and dynamics of Mediator and Pol II. Mediator forms small transient clusters and large stable clusters, while Pol II also forms similar clusters. The stable clusters are colocalized and show dynamic behavior, including coalescence, rapid recovery in FRAP assays, and sensitivity to hexanediol. These findings suggest that Mediator and Pol II form in vivo condensates that may facilitate transcriptional regulation. The study also shows that Mediator clusters can dynamically interact with actively transcribing genes, supporting a dynamic kissing model where Mediator clusters occasionally colocalize with gene loci. The results imply that large Mediator clusters at enhancers can transiently interact with the transcription apparatus at promoters, influencing gene control mechanisms. The findings highlight the importance of spatial organization and dynamics in transcriptional regulation.