Aims: To examine the genetic diversity and relatedness among pepper accessions using agro-morphological markers. Study Design: Augmented design with single rows of each genotype. Place and Duration of Study: Research field, CSIR-Savanna Agricultural Research Institute, Nyankpala-Tamale, Ghana, May to October, 2012. Methodology: Fifty local pepper genotypes from different agro-ecological zones in Ghana were characterized using 35 agro-morphological (11 quantitative and 24 qualitative) traits using standard descriptors for Capsicum sp. For quantitative traits, measurements were recorded on ten tagged plants and the mean value used while four tagged plants were scored for the qualitative traits. Results: The first three principal components accounted for 59.61% of the total genetic variance among the genotypes with the larger part of the variance explained by fruit pedicel width, fruit weight, fruit length, plant height, stem diameter, fruit pedicel length and fruit width. For qualitative traits, the first three principal components contributed to 51.65% of the total genetic variance with leaf pubescence density, fruit position, calyx annular constriction and filament colour as the most important parameters. The study showed a great variation in fruit traits revealing six fruit shapes and four fruit colours. Fruit weight exhibited positive and significant correlations with yield components such as fruit length and fruit width. Conclusion: The study has shown that morphological markers are effective tools in studying genetic diversity in Capsicum species. This observed diversity among the pepper genotypes would therefore be used for improving pepper through hybridization and selection.