Provided are a method, system, and article of manufacture for controlling a first storage system receiving commands from a first and second managers to create a consistency group with a second storage system. Host writes are received at the first storage system, wherein the first storage system includes a first storage system primary site and a first storage system secondary site. The first storage system sends the host writes from the first storage system primary site to the first storage system secondary site. Host write operations are quiesced at the first storage system in response to a first command from a first manager. Host write operations are resumed at the first storage system in response to receiving a second command from the first manager. The first storage system receives a run command with a marker, wherein the marker indicates a cycle number to control the cycles of the first and second storage systems. The first storage system sends the marker from the first storage system primary site to the first storage system secondary site. The first storage system sends the marker to a second manager. The first storage system applies the host writes to the first storage system secondary site. The first storage system sends a first message to the first storage system primary site from the first storage system secondary site after completing the applying of the host writes. The first storage system sends a second message to the first manager indicating whether conformation was received from the first storage system secondary site that the host writes were applied.