Critical political economy views the global expansion of transgenic agriculture as emblematic of a new phase of transnational capital accumulation. This study seeks to understand resistance to agricultural biotechnology in Guatemala. There, despite backing from US-based Monsanto and a weakened Mayan indigenous movement, transgenic crop cultivation remains illegal. I argue that opposition to transgenic maize, by raising concerns over risks to biodiversity and farmer livelihoods, is leading to a re-articulation of Mayan movements and their increasing identification with environmental and campesino (or peasant) struggles. These “knowledge alliances” are shaping national debates over the technology and hindering the advancement of the neoliberal food regime.