Technical Abstract: In Africa, many smallholder farmers grow open pollinated maize varieties (OPVs), as they allow seed recycling and out-yield traditional farmer’s (unimproved) landraces. One popular OPV, ZM521 released by the International Maize and Wheat Improvement Center (CIMMYT), has been provided to farmers, often by Non-Governmental Organizations (NGOs) who help farmers gain access to improved seeds, particularly following disasters in which original seed is lost. However, NGOs often rely on local seed suppliers to provide the seed, and in some years the seeds provided to the farmers are suspected not to be of the promised variety. Here we present methodology to prove within a high level of confidence if two samples of seeds are the same genetic population or not, despite the difficulties involved in fingerprinting heterologous populations. In addition to the actual heterogeneity within populations, these difficulties include sampling errors, differences due to seed sources (the fields or years in which the seeds were multiplied), and possible mixing of seed or flow of pollen from neighboring fields. Despite these confounding sources of variation, we show the possibility to conclusively identify each population. This methodology will allow breeders, seed companies, government agencies and NGOs to ensure that the correct seed of high yielding, locally adapted OPVs reach farmers and generate the highest yields possible in their fields.