Black foot disease is a common and destructive root disease of grapevine caused by a multitude of cylindrocarpon-like fungi in many viticultural areas of the world. This study identified 12 cylindrocarpon-like fungal species across five genera associated with black foot disease of grapevine and other diverse root diseases of fruit and nut crops in the Central Valley Region of California. Morphological observations paired with multi-locus sequence typing of four loci, internal transcribed spacer region of nuclear rDNA ITS1-5.8S-ITS2 (ITS), beta-tubulin (), translation elongation factor 1-alpha (), and histone (), revealed 10 previously described species; , , . , . , . , . , . , , . , . , and two new species, ., and . Phylogenetic analyses of the ITS++ combined dataset, a commonly employed dataset used to identify filamentous ascomycete fungi, was unable to assign some species, with significant support, in the genus , while all other species in other genera were confidently identified. The marker was essential either singly or in conjunction with the aforementioned genes for accurate identification of most species. Results from isolations of diseased plant tissues revealed potential new host associations for almost all fungi recovered in this study. This work is the basis for future studies on the epidemiology and biology of these important and destructive plant pathogens.