Alliance Management consists of an Alliance Management Team (AMT) that is the governing body for the organization; an Alliance Coordination Team that reports on progress of the Priority Issue Teams to the AMT; and a Headquarters Office to keep the organization running smoothly and to maintain the requirements of a 501(c)3 organization.

All five Gulf States have representation on the AMT as well as the federal partners including the Environmental Protection Agency, National Oceanic and Atmospheric Administration and the

Department of the Interior. The AMT determines the priority issues that will enhance the ecologic and economic health of the Gulf region on behalf of the Gulf State Governors. The AMT is led by a series of rotating chair persons from each of the Gulf States. Leadership rotated to the State of Florida in June 2018.

Other committees that support the way the Gulf of Mexico Alliance operates includes a Federal Working Group, a Data Management Advisory Committee, a Public Relations Committee, and a Business Advisory Council.