The Gibberella fujikuroi complex (GFC) is a monophyletic taxon that includes an assemblage of Fusarium species with similar and overlapping morphological traits that complicates their differentiation. Most of the species in this complex are associated with devastating diseases of many economically important plants. They also produce a remarkably wide range of secondary metabolites or mycotoxins that contaminate food/feed worldwide and can subsequently cause a variety of diseases in humans and animals. Recent developments in molecular systematics have revealed that the Gibberella fujikuroi complex includes at least 50 distinct species or phylogenetic lineages. Of these, 34 species have been formally described using morphological characters, 10 have been also described based on sexual fertility and at least 20 species produce one or more mycotoxins. Here, we review the most important criteria for recognising and defining Fusarium species in the Gibberella fujikuroi complex. We also consider the diversity within this complex, specifically from an evolutionary point of view. We, therefore, discuss the morphological, biological and phylogenetic diversity in the Gibberella fujikuroi complex, by reviewing these properties together with aspects such as mycotoxicology, geographic distribution and host/substrate preference of the various Fusarium species with respect to their phylogeny.