Californian thistle (Cirisum arvense) is a troublesome weed in pastures and cropping systems. The fungal biocontrol agent Puccinia punctiformis, commonly referred to as thistle rust, performs inconsistently on C. arvense. Problems with P. punctiformis establishment and control of C. arvense may be attributable to differing plant endophytic populations in various environments. This article provides an overview of the relationships between endophytes and their host, but also between endophytes and pathogens with a focus on rust pathogens. This review provides insights into reasons why P. punctiformis performs inconsistently and identifies gaps in our knowledge. Filling these gaps may help to improve performance of this classical fungal biocontrol agent. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.