During the last 20 years, the biodiversity international legal and institutional framework emphasized countries’ sovereign rights and indigenous and community rights on biodiversity and traditional knowledge. However, a critical examination of its practical application in Colombia illustrates the constraints to develop the country’s endogenous scientific research capacity to govern its resources and to effectively protect indigenous rights. The Colombian case shows that sovereignty and indigenous rights tend to be diluted, particularly in the context of free trade agreements with the United States. It is shown that, in the context of international law and bilateral market agreements, sovereign rights and indigenous rights tend to be eroded due to the adoption of a strong intellectual property rights regime that favors biotechnology transnational capital interests.