Fungal diseases constitute some of the most critical threats in relation to global agricultural production, with the consequence of causing severe losses in yield, post-harvest decay, and being a threat to food security. The main management approaches are based on the use of chemical fungicides that, in spite of being initially effective, are increasingly questioned with the development of resistance to pathogens, residual toxicity, and environmental issues. The pressure on more vigorous and environmentally friendly solutions requires one to understand further the intrinsic plant defense mechanisms as the foundation for the sustainable management of diseases. Biochemical resistance is a very important part of plant defense, as it consists of constitutive and inducible defense mechanisms. These reactions involve the production of pathogenesis-related (PR) proteins, the build-up of phytoalexins, the activation of phenylpropanoid pathway proteins, including phenylalanine ammonia-lyase (PAL), peroxidase (POD), and polyphenol oxidase (PPO), and the increased production of reactive oxygen species (ROS), which causes hypersensitive cell death and limits pathogen proliferation. Plants that are highly biochemically resistant can delay or inhibit colonization by fungal pathogens, and hence they are the most critical breeding targets in resistance breeding programs of the cultivars. These dynamics of compatible and incompatible interactions between plants and fungi are thus essential to discover the molecular markers of resistance. The objective of this chapter is to critically compare the biochemical defense mechanisms of the selected genotypes of the plants against economically significant fungal pathogens. It also includes the complex dialogue between plant and fungal activity that sheds light on metabolites that can be targeted by plant breeders for the development of disease-resistant plants. This chapter provides a valuable foundation for biotechnologists and pathologists to identify biomarkers and understand fungal-plant interactions.