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Although vanilla originated from Mexico and an important pathogen for this plant is Fusarium oxysporum f. sp. vanilla, studies concerning their association are limited. Previous reports on agents that cause root and stem rot in vanilla clearly indicate that Fusarium species are associated with this disease. During 2009 and 2010 in Papantla, which is the greatest vanilla–producing region of Mexico, the fungus was isolated from vanilla roots and stems that showed symptoms of the disease. From 189 isolates of Fusarium, 11 morphologically different colonies were selected to verify the species of each colony by microscopic observation of their morphological characteristics when cultivated on SNA and PDA media and by amplifying and sequencing their ITS regions. The detected species corresponded to F. proliferatum, Fusarium sp., F. oxysporum f. sp. vanillae (which was the most numerous and most pathogenic to vanilla stems and leaves), an undetermined species of Fusarium, and F. proliferatum, which showed no evidence of producing disease symptoms.