Black root rot, caused by soilborne fungal pathogens in the Nectriaceae family, is a severe disease of avocado nursery trees and orchard transplants. Rapid decline and death of young trees within a year after planting is typical, with symptoms including black, rotten and necrotic roots, tree stunting, leaf wilt, chlorosis, necrosis, and leaf drop prior to tree death. This study identified the nectriaceous fungal genera and species associated with black root rot of avocado, investigated the phylogeny of the genera and determined pathogens to avocado. Fungal isolates were collected from symptomatic avocado roots from orchards and nurseries in all growing regions in Australia, and from other hosts. The identities of 153 isolates were confirmed with Bayesian inference and Maximum likelihood phylogenetic analyses of concatenated ITS, β-tubulin and histone H3 gene loci. The nectriaceous fungi found associated with black root rot include Calonectria ilicicola, Dactylonectria macrodiyma, D. anthuriicola, D. novozelandica, D. pauciseptata, D. vitis, Gliocladiopsis peggii, G. forsbergii, G. whileyi, Cylindrocladiella pseudoinfestans, Ilyonectria sp. and Mariannaea humicola. Comprehensive phylogenetic analyses revealed additional putative new species and species complexes in each genus. Glasshouse pathogenicity tests confirmed Ca. ilicicola isolated from avocado, papaya, peanut and custard apple, and Calonectria sp. from blueberry, caused significant root rot in avocado cv. Reed seedlings within 5 weeks of inoculation. Dactylonectria macrodidyma, D. novozelandica, D. pauciseptata and D. anthuriicola were confirmed as pathogens, causing black root rot within 9 weeks. Cylindrocladiella pseudoinfestans, G. peggii and isolates of Ilyonectria sp. were non-pathogenic.