The common bean (Phaseolus vulgaris L.) is a key crop for food security in Mexico, yet its genetic resources remain poorly characterized in rural areas with high agrobiodiversity. Using genotyping-by-sequencing, we assessed genetic diversity, population structure, and gene flow among wild populations (W), traditional landraces (L), and commercial varieties exchanged through local markets (M), contrasting these populations with a sample of improved varieties (I). We analyzed a total of 78 individuals and 18,951 neutral SNPs. Population analyses (sNMF, PCoA, Neighbor-Joining, AMOVA) revealed strong differentiation between wild populations and cultivated forms (landraces and markets) (FstL-W = 0.704 and FstM-W = 0.601), whereas landraces and market varieties were weakly differentiated (FstL-M = 0.059). Wild populations exhibited the highest genetic diversity, with the greatest proportion of polymorphic loci (%PW = 56.6), expected heterozygosity (HeW = 0.49), and nucleotide diversity (πW = 0.55). Cultivated forms showed lower diversity across all parameters, although levels exceeded those previously reported for Guerrero and other Mexican regions. Gene flow was limited between wild and cultivated forms but high between landraces and market varieties (NmL-M = 7.877), highlighting the role of seed exchange networks in maintaining connectivity and diversity. These findings underscore the importance of conserving wild populations, landraces, and traditional seed systems to strengthen crop resilience and food security under climate change.