The genetic diversity among twenty hot pepper (Capsicum spp. L.) accessions from eight different geographic locations in Ghana, was studied using molecular and phenotypic characteristics to evaluate their genetic relationships. Using the International Plant Genetic Resources Institute descriptor list for capsicum the genetic diversity in 13 quantitative and 22 qualitative traits were assessed. Fifteen SSR markers were used to validate the molecular identities of the pepper collections. Principal component analysis indicated that few characteristics, including fruit length, mature leaf length, plant height, plant canopy width, quantity of seeds in each fruit also had major impact on genetic variation. All accessions were recognised as distinct with no duplications after a dendrogram categorized pepper genotypes into cultivated and wild based on their morphological characteristics. Fruit weight, fruit breadth, and fruit length were shown to be strongly correlated with each other as well as with plant canopy width, plant height, and length and width of mature leaves. A negative correlation was detected between fruit length and days required for 50% fruiting and flowering. By utilizing SSR analysis and dendogram, genotypes UPP 01 and NOR 03 from separate clusters can be selected for crossing, which would produce increased heterosis and segregants for further use.

Keywords: Agro-morphological, Simple sequence repeat, molecular, characterization, hot pepper