Phaseolus vulgaris L. (common bean) is a valuable and highly nutritious food legume which exhibits a wide variety of seed coat patterns and colors. Such colors are controlled by a group of specific genes that regulate the flavonol and anthocyanin biosynthetic pathways. The current study aims to describe genetic and molecular analysis of three seed types of P. vulgaris var. including strike, contender, and wonder types that possess different seed coats colors (creamy, brown to deep brown, and reddish spotty (pinto) beans. We assessed the phenotypic characteristics of the seeds and seed coats based on seed germination and seedling growth parameters from one hand and macro, micro-phenotypic aspects of seed coat using stereomicroscope and scanning electron microscope (SEM) from other hand. The results indicated that all markers used from phenotypic to DNA-based molecular markers differ in their resolving power to detect genetic variations, identification, genetic structure, and type of data they generate for each species. Phenotypical and protein-based markers were dependent on the gene expression of DNA at exons (coding) region only. On the other hand, the DNA-based markers were dependent on coding (exons) and non-coding (intron) regions and are not governed by above external factors. In conclusion, the DNA-based markers seemed to be the best-suited molecular assay for fingerprinting and assessing genetic structure of each one of P. vulgaris L. variety with high accuracy. Also, P. vulgaris var. with brown to deep brown seed coat color was more pronounced than the other two varieties.