Biofuel crops such as napiergrass possess traits characteristic of invasive plant species, raising concern that biofuels might escape cultivation and invade surrounding agricultural and natural areas. Napiergrass biofuel types are being developed to have reduced invasion risk, but these might be cultivated in areas where naturalized populations of this species are already present. The successful management of napiergrass biofuel plantations will therefore require techniques to monitor for escaped biofuels as distinguished from existing naturalized populations. Here we used 20 microsatellite DNA markers developed for pearl millet to genotype 16 entries of napiergrass, including naturalized populations and accessions selected for biofuel traits. Use of the markers showed a clear genetic separation between the biofuel types and naturalized entries and revealed naturalized populations undergoing genetic isolation by distance. These findings demonstrated the utility of microsatellite marker transfer in the development of an important tool for managing the invasion risk of a potential biofuel crop.