The Pathology division came into existence as Mycology division during 1954, later renamed in 1969. The Division focuses on sustainable disease management in coffee through scientific and eco-friendly approaches. Its work includes mapping Coffee Leaf Rust (CLR) races, screening new hybrids for disease resistance, evaluating fungicides, and promoting bio-control agents such as Trichoderma.

Key achievements include identifying effective fungicides like Alkaline Bordeaux Mixture and Hexaconazole, developing integrated spray schedules using botanicals and bioagents, and isolated 39 CLR races. The Division also continuously monitors Arabica and Robusta germplasm for disease resistance and validates new fungicide molecules in the field, strengthening Integrated Disease Management (IDM) strategies for resilient and climate-smart coffee cultivation.