Characterization of 61 Macedonian runner bean (Phaseolus coccineus L.) local cultivars was performed by using nine quantitative and qualitative descriptors of the seeds: seed length, seed height, seed width, 100 seed weight, seed coat color, seed coat pattern, seed coat pattern color, seed hilum ring color and seed shape. Principal component analysis and two-way cluster analysis were performed in order to classify the germplasm based on the analyzed traits. The first three principal components explained 81.3% of the morphological variability of the genotypes. PCs 1 and 2 jointly explained 66.8% of the total variance for the analyzed traits. The qualitative traits seed coat color, seed coat pattern color, seed coat pattern and seed hilum ring color were the major contributors to PC1, while the quantitative traits 100 seed weight, seed length, seed height and seed width mainly contributed to PC2. Based on the two-way cluster analysis, the genotypes were separated in ten major clusters, each comprising a different number of subclusters and genotypes. The results obtained from this study are providing useful information on the extent of genetic diversity of Macedonian runner bean landraces, which can be used for development of new cultivars with desirable seed characteristics.