Dry bean breeding programs have made significant advances in combating both abiotic and biotic stresses as well as improving plant architectural traits via selective breeding. Flooding can cause complete crop loss in dry bean. On the other hand, breeding for an upright architecture in dry bean has been a breeding target in several programs. However, the stem cell wall components underlying this change have yet to be studied. This research focused on analyzing the cell wall components that might be involved in dry bean architecture as well as pre-germination flooding tolerance in dry bean. For the plant architecture study, two significant genomic regions were identified on Pv07 and Pv08 associated with lignin accumulation in dry bean. For the pre-germination flooding study, one unpigmented seed coat genotype (Verano) and three pigmented seed coat genotypes (Indeterminate Jamaica Red, Durango, and Midnight) had germination rates similar to that of the tolerant check.