Understanding genetic variability in pepper (Capsicum annuum L.) will contribute to effective breeding efforts, especially in northern Ghana, where pepper contributes significantly to the smallholder farmer's income. This study evaluated 13 morphological traits including those related to vegetative, inflorescence, and fruit-related within a collection of 40 pepper genotypes from five different locations in the northern region of Ghana. Significant variations (p < 0.05) were detected among the pepper genotypes for all measured traits. A strong positive correlation was detected between days to 50 % flowering and days to 50 % fruiting for both the rainfed (r = 0.87) and irrigated (r = 0.73) conditions. High performance of the genotypes at the vegetative and inflorescence stages was observed in the dry season, with low fruiting performance (number of fruits per plant, fresh weight, and dry weight). Multivariate analysis revealed that 60.54 % and 54.63 % variations were explained by the first three principal components, respectively. Three main clusters were identified, with linear relationships and no distinct separation pattern based on location, thus providing an opportunity to remove duplicate genotypes in the studied region. The results indicated that the selection of genotypes with better agronomic traits could be achieved from this pepper gene pool. The present findings may pave the way for better utilization and production of pepper, leading to improved adaptation in the region.