Forward genetic screens hold great promise for identifying mutants with cell wall phenotypes of interest; however, the time and cost required to physically map these mutations can be considerable, if not prohibitive.  We have therefore developed a method to quickly and efficiently map recessive mutations identified in such screens using next-generation genomic technology, and validated the approach by mapping Arabidopsis cell wall mutations.  Briefly, F2 lines generated by crossing a mutant plant to a mapping line are sequenced en masse using a next-generation sequencing platform such as the Illumina Genome Analyzer, producing tens of millions of short reads that are aligned to a reference genome using existing public domain software. We then apply our approach which identifies the mutation of interest by examining the genomic distribution of SNPs associated with the mapping and mutant genomes.  This method takes advantage of the fact that recombination between the mutant and mapping lines will result in a random admixture of both genomes, visible as an abundance of single nucleotide polymorphisms (SNPs) throughout the F2 genomes, except for a region surrounding the mutation of interest.  Moreover, individual SNP properties can then be used to further refine the region around the mutation.  We tested our approach on three Arabidopsis cell wall mutants that were being mapped by traditional mapped-based cloning techniques and identified 5, 1, and 2 candidate SNPs for the three mutants respectively.  In each case, the causal mutation was present in our candidate list and functionally confirmed in planta.