Successful development of plants resistant to salinity stress is problematic as a result of the complex polygenic natures of salt tolerance. Previously, alkaline extracts of the brown seaweed Ascophyllum nodosum have shown promise in enhancing plant tolerance toward abiotic stresses. To understand the underlying molecular mechanisms, the whole genome transcriptome of Arabidopsis undergoing salt stress was analyzed by microarray analysis after treatment with the chemical components of A. nodosum extracts (ANE). Treatment with ANE induced many positive regulators of salt tolerance in addition to downregulating numerous other genes. Using T-DNA insertion mutants within these downregulated genes, we examined the potential for a novel source of enhanced NaCl tolerance through removal of negative regulators of NaCl stress responses within Arabidopsis. Several potential target mutations were identified with enhanced salt-tolerant phenotypes. A T-DNA insertion within the promoter of a putative Pectin Methyl Esterase Inhibitor (PMEI) gene (At1g62760) was found to be resistant to salinity stress and was further characterized. This T-DNA insertion mutant was designated as pmei1-1. The phenotype of pmei1-1 seedlings included increased primary root growth in vitro and improved biomass accumulation under NaCl stress. Additionally, modified transcript levels of dehydration-responsive genes, including RD29A, were observed in pmei1-1 plants. Taken together, these results suggest a role for PMEI as a negative regulator of NaCl resistance and that chemical stress-induced transcriptome analysis may lead to identification of additional novel regulators of abiotic stress tolerance in plants, the use of which would have significant implications for agriculture globally.