Crop disease management in smart agriculture involves applying and using new technologies to reduce the impact of diseases on the quality of products. Coffee rust is a disease that factors such as poor agronomic management activities and climate conditions may favor. Therefore, it is crucial to identify the relationships between these factors and this disease to learn how to face its consequences and build intelligent systems to provide appropriate management or help farmers and experts make decisions accordingly. Nevertheless, there are no studies in the literature that propose ontologies to model these factors and coffee rust. This paper presents a new ontology called RustOnt to help experts more accurately model data, expressions, and samples related to coffee rust and apply it whilst taking into account the geographical location where the ontology is adopted. Consequently, this ontology is crucial for coffee rust monitoring and management by means of smart agriculture systems. RustOnt was successfully evaluated considering quality criteria such as clarity, consistency, modularity, and competence against a set of initial requirements for which it was built.