The federal Endangered Species Act (ESA) is nearly silent regarding its potential application in Indian Country. But by the mid-1990s, the ESA had proven to be a source of serious concern for Indian tribes. In 1997, as the culmination of months of negotiations between agency officials and tribal representatives, the Secretaries of the Interior and of Commerce jointly issued Secretarial Order 3206 (SO 3206), entitled “American Indian Tribal Rights, Federal-Tribal Trust Responsibilities, and the Endangered Species Act.” The order sought to harmonize the federal trust responsibility to tribes and the statutory missions of the Departments of the Interior and Commerce in implementing the ESA. This paper considers whether the order has lived up to its promise of true bilateralism between the United States and sovereign tribal governments regarding their rights vís-a-vís the ESA process. It reviews the key requirements of the ESA, pertinent executive orders, and SO 3206 itself. It analyzes government-to-government relations in several cases of “final rule” critical habitat designation and through a review of scholarly literature. Further, it discusses the difference tribes can make by creating and implementing their own habitat management plans, as alternatives to designation of critical habitat on Indian lands, and by actively partnering with the U.S. Fish and Wildlife Service and National Marine Conservation Service. The author concludes that while SO 3206 has not yet lived up to its full promise, it is making a difference by assisting federal land managers and sovereign tribal governments in building stronger working relationships while protecting the environment.