The Fusarium lateritium species complex (FLSC) currently comprises 11 phylogenetic species, including accepted names such as F. lateritium, F. sarcochroum, and F. stilboides, which have mostly been reported in association with citrus and coffee. Many varieties were documented by Wollenweber & Reinking (1935), which is indicative of a wider diversity of species within this group. The lack of type material in some cases, especially for the older names, means that definition by molecular phylogeny is very difficult. In the present study, we examined 179 strains related to F. lateritium from different countries and substrates. Historic reference material, including representative strains from the Wollenweber & Reinking (1935) varieties were included in this study, DNA sequences were generated for comparison, and the morphology correlated with original descriptions to enable the correct application of older names. Strains were characterized by multi-gene phylogenetic analyses based on fragments of the β-tubulin (tub2), calmodulin (CaM), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1) genes, evaluation of morphological characters and host-substrate preferences. The biological species concept was tested by crossings in vitro. Strains previously identified as F. lateritium, F. stilboides, or one of their varieties based on morphology, were found to belong to 16 species in the FLSC, but also to species from six other species complexes (SC), including the F. citricola SC, F. heterosporum SC, F. incarnatum-equiseti SC, F. redolens SC, F. sambucinum SC, and the F. tricinctum SC.