The resilience of cell walls to enzymatic hydrolysis of carbohydrates is a major impediment to the economical production of ligno-cellulosic ethanol. The identification of DNA polymorphisms associated to increased cell wall (CW) degradability will accelerate the development of alfalfa (Medicago sativa L.) cultivars with superior ethanol conversion yields. Genotypes with high (D+) and low (D-) cell wall degradability were identified within a biomass-type population. Screening was based on near-infrared reflectance spectroscopy (NIRS) predictions of CW glucose released by enzymatic saccharification. We used sequence-related amplified polymorphism (SRAP) to search for DNA variations associated to differences in enzymatically released glucose. A bulk segregant analysis of D+, D- and randomly chosen genotypes (25 plants/bulk) was performed using 42 SRAP primer pair combinations. Several polymorphisms that varied in intensity between high and low CW degradability were uncovered. Both increased and decreased intensity in D+ and D- polymorphisms were observed. Analyses of DNA polymorphisms among genotypes of bulk groups confirm differences in genotypic frequency. Our results show that DNA regions associated to cell wall degradability can be identified. Research is currently under way to sequence polymorphic fragments and search for homologies with sequences in gene databases.