Brassica is a very important plant genus, not only as a source of oil and protein for human and animal nutrition, but also as a potential source of allelochemical control for a variety of soil-born pests. The discovery of anticarcinogenic effects of Brassica’s secondary metabolites has increased the importance of this genus. Brassica also plays a very important role in ecosystems. Arabidopsis is one of the most important model plants suitable to study the interaction between plant and pathogens. Availability of numerous collections and mutants help in using this plant in developing novel crop protection strategies. The objective of this paper is to review the interaction between Brassica and Arabidopsis plants with pathogenic fungi and to explain the role of glucosinolates, phytoalexins and other secondary metabolites in defense against these detrimental pathogenic fungi. The advent of new technologies for the analysis of gene expression combined with the recent progress in exploring the complete genome sequence in many plants have led to a good understanding of the plant-fungi interactions. Metabolite measurements, metabolomic profiling and multivariate analysis are considered as promising approaches for evaluating particular signaling pathways with defense responses.