The Botryosphaeriales are amongst the most widespread, common and important fungal pathogens of woody plants. Many are also known to exist as endophytes in healthy plant tissues. This special issue highlights a number of key themes in the study of this group of fungi. In particular, there have been dramatic taxonomic changes over the past decade; from one family to nine (including two in this special issue) and from 10 to 33 genera known from culture. It is also clear from many studies that neither morphology nor single locus sequence data are sufficient to define taxa. This problem is exacerbated by the increasing recognition of cryptic species and hybrids (as highlighted for the first time in this special issue). It is futile that management strategies, including quarantine, continue to rely on outdated taxonomic definitions and identification tools. This is especially true in light of growing evidence that many species continue to be moved globally as endophytes in plants and plant products. A well defined natural classification and an extensive collection of tools to study the Botryosphaeriaceae, including a growing number of genomes, now provide a springboard for a much deeper exploration of their biology, biogeography and host associations.