Kenya is currently in the process of introducing genetically modified maize (Bt maize). A major concern is that the Bt gene might cross into local varieties through cross pollination. Current regulatory strategies to ensure coexistence of the two cropping systems at the farm level rely on spatial isolation measures-separation distances and/or buffer zones. However, the interaction of practical measures and costs of spatial isolation with the farmer’s economic incentive to plant a Bt maize crop have not been studied in Kenya. The purpose of this study was to analyze the technical and economic feasibility of the implementation of spatial coexistence measures. Using spatial geo-referenced data from the actual agricultural landscape in lowland coastal Kenya, the study finds that flexible separation distances hold the possibility of ensuring coexistence in the region, but will be difficult to implement. Rigid buffer strips on the other hand are not consistent with the producers’ economic incentive to plant a Bt maize crop.