Eight different saline tolerant strains of Arbuscular Mycorrhizal Fungi (AMF) were recovered from rhizosphere soil of plants growing in coastal saline soils in the West Coast of Kerala, India. They were characterized by subjecting spore extracts to polyacrylamide gel electrophoresis and selective enzyme staining. The activity of the Malate dehydrogenase (MDH) was measured after separation of the fungal enzymes on polyacrylamide gels. The banding patterns of malate dehydrogenase in these isolates were studied to identify the intrageneric variation in the activity of enzymes. The results showed only minor variations in the activity of the enzyme in all AMF species. Four distinct zones of MDH activity were detected on the gels based on the patterns of electrophoresis variations among the eight species of AM fungi. The study revealed that isoenzymic studies are useful for the differentiation and identification of AMF genera and species.