Cotton genetically engineered to express antifungal peptides should decrease susceptibility to fungal pathogens, on the other hand they also have the potential to affect mycorrhizal associations important in cotton development and yield. This paper will report the effects of antifungal peptides engineer into tobacco as a model system on mycorrhizal associations. The specific anti-fungal peptides include a chitosanase, two magainin analogs and an analog of cecropin. The chitosanase is a hydrolytic enzyme that attachs fungal cell walls containing chitosan, while the other three are amall peptides that insert into microbial membranes and lead to loss of membrane integrity.