Plant pathogens are playing an increasing role in classical biological control of weeds worldwide. This paper presents an explicit framework consisting of various interconnected steps to facilitate and streamline the selection process for pathogen agents. It also highlights and discusses critical issues associated with the various steps of the selection framework such as the climatic‐matching approach to find well‐adapted agents, host–pathogen matching and pathogen genetic structure. Processes and issues relating to the selection of pathogens are then contrasted with those usually adopted for arthropod selection in weed biological control. In both cases optimising the level of genetic diversity in introduced agents is seen as beneficial to biological control success. The difference in regulatory approach for multiple and genetically pure pathogen strains vs. genetically variable arthropod agents is highlighted for further scientific debate.