This article examines the effects of the ambiguous and limited recognition of Indigenous law in Mexico on Indigenous women’s efforts to attain greater gender justice. Mexico constitutionally recognizes indigenous peoples’ right to self-determination and has adopted both the UN Declaration on the Rights of Indigenous Peoples and ILO Convention 169. However, the State still has not recognized Indigenous peoples’ right to territory and limits self-governance rights in practice. The author presents case studies to demonstrate the inconsistency of State treatment of Indigenous law. State authorities have used cases of gender discrimination within customary legal systems to justify limiting Indigenous autonomy. Meanwhile, it has denied Indigenous women access to justice and has promoted policies of economic development that expose Indigenous women to greater harm. The ambiguity of recognition of Indigenous governance means that Indigenous people are increasingly subject to persecution and criminalization for exercising their nationally and internationally recognized rights to autonomy.