To protect against pathogens plants have an innate immune system. One of the defense mechanisms, Pattern Triggered Immunity (PTI), prevents non-adapted microbes from infecting plants. The surface pattern recognition receptors (PRRs) firstly recognize pathogen associated molecular patterns (PAMPs). PAMP recognition stimulates ion transportation through plasma membrane and enhances activation of protein phosphorylation/dephosphorylation process in which calcium-dependent protein kinase (CDPKs) and mitogen-activated protein kinase (MAPKs). Thus the perception of PAMPs induces an extracellular oxidative burst, which requires the function of NADPH oxidase for production of membrane impermeable O2- in the apoplast, which is then converted to H2O2 by the activity of peroxidase. H2O2 functions as a signaling molecule for the activation of defense responses as well as antimicrobial agent. H2O2 also serves for cell wall lignification (barrier for pathogen penetration). In turn, plants have another layer of immunity based on the direct or indirect recognition of microbial effectors by host receptors called Resistance (R) proteins.
Phytohormones also play a crucial role in disease resistance. The main hormones playing a role in plant defense are: salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA). These hormones are able to modulate plant resistance by metabolic pathways or stimulating the expression of defense-related genes, such as PR genes.

Reactive Oxygen Species (ROS) also play a central role in plant defense against various pathogen.