Frafra potato (Solenostemon rotundifolius) is an important food crop indigenous to Western Africa and a member of the Labiaceae (mint) family. It is nutrient-rich and drought tolerant; however, despite its potential as a food security crop, it has not received the research support needed to promote its widespread adoption and safeguard its diversity. As a result, Frafra potato is becoming extinct and restricted to indigenous communities where it holds traditional importance. It is imperative that conservation methods are explored, but before then, the genetic diversity of the species should be assessed. The objectives of this study were to develop simple sequence repeats (SSRs) for Frafra potato from de novo sequencing of the genome, and to provide a preliminary assessment of genetic diversity of Frafra potato in Ghana. To this end, 57 accessions of Frafra potato obtained from three geographic regions of Ghana were characterized using 15 discovered microsatellites. Forty-six multilocus genotypes (MLGs) were identified among the 57 accessions. The genetic diversity among the MLGs was moderate-to-high. Preliminary evaluation of accessions from the three collection zones indicated the presence of population structure among Frafra potato individuals collected in Ghana, Africa.