This paper explores the consequences of ignoring pre-existing un-official and illegal networks for external interventions with approaches to sustainable management of natural resources in marginalized areas of the developing world. To do so, it assesses the effects of a public Research & Development (R&D) intervention aimed at promoting sustainable exploitation and trade of aloe-based products in the semi-arid Baringo County (Kenya), and how it interacted with an existing illegal supply chain dedicated to the exploitation of indigenous aloe species. Data were collected through a qualitative and participatory assessment that was conducted between April and November 2012, using an analytical framework and guidelines derived from the innovation system perspective. The study shows that geographical disparities in the effect of external intervention are the result of unplanned interactions between project stakeholders and actors from the illegal supply chain. The Baringo aloe case suggests that networks involved in illegal trade of natural resources should not be ignored or sidelined by R&D interventions but should on the contrary be supported to allow them to evolve towards certified trade.