Plant pathogens frequently do not operate alone when causing diseases. Since the infection process is affected by the interaction between members of the parasite community, this question asks about the efficiency of disease control strategies which are usually tailored to manage only one microbial pathogen at a time. Fungi and oomycetes are among plant disease's most prevalent and damaging causal agents. With the increasing ability to distinguish individual species, thanks to new high-throughput molecular tools, numerous diseases once attributed to a single species are now recognized as being caused by complexes of fungal phytopathogens. How should we approach the study of these complexes? What tools and methodologies are needed to characterize them and decipher their functional interactions? How can we understand and master the drivers of these coinfections and their dynamics under field conditions? Here, we review the current literature on fungal disease complexes to define their commonalities and address some of the current challenges regarding the identification of preferential associations among fungal species indicative of a disease complex and its community dynamics and regulation. This review highlights that fungal species complexes are highly dynamic at geographic and temporal scales and that human actions contributed to the dissemination of new members of species complexes worldwide and to disequilibrium within species complexes, often resulting in more damaging diseases. This review also points to the generally insufficient (or lacking) knowledge of the diversity, dynamics, and functioning of fungal disease complexes, and the risks linked with inappropriate management strategies focusing on only one dominant member of the complex.