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The objective of the current research was to characterize the common bean in agricultural fields planted with common bean landraces from the semi-arid Mexican high plateau using both morphological and amplified fragment length polymorphism (AFLPs) data. The morphological traits were discriminating and exhibited the clustering of 150 accessions based on the geographic origin and seed coat color. AFLP primer combinations exhibited a polymorphic range between 0.292 (E-AGG + M-ACT) and 0.375 (E-ACA + M-AGA). The frequency and distribution of the polymorphic fragments allowed the detection of a larger number of rare fragments in accessions 121 and 111 (Flor de Mayo and black common beans, respectively). The analysis of genetic relationships, analysis of molecular variance (AMOVA), and Powell’s diversity index confirmed a broad genetic basis for the germplasm of the common bean from the semi-arid Mexican high plateau. The clustering and principal coordinate analyses demonstrated a strong genetic relationship among the collected common bean landraces based on the similarity in the variety name, origin, and seed coat color, demonstrating the influence of different cultivation practices in the two regions and the adaptation of P. vulgaris to the agroclimatic conditions of the semi-arid Mexican high plateau.