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Gunung Kidul is the centre of cassava production. However, due to its Mediterranean soil type, it is regarded as a non-fertile soil as it was formed from the decay of limestone, has low organic matter, dry texture, brittle, and pH value of neutral to basic. Mycorrhizal inoculation is known to increase plant production, however, the effectivity is affected by the plant variety and mycorrhizal sources. This study aims to understand the interaction between various mycorrhizal sources and three local cassava varieties of Gunung Kidul, specifically on their compatibility, population, mycorrhizal diversity, and their effect on cassava growth. The experiments were conducted based on Completely Randomised Design (CRD) with experimental factors using three treatments in triplicates. The experimental factors included three cassava varieties (Mentega, Kirik, and Ketan) and various sources of mycorrhiza (indigenous Mediteran soil of Gunungkidul, the rhizosphere of pandan plants of Bugel beach, and commercial mycorrhizal inoculant). The results demonstrated that among the interactions of various mycorrhizas with three local cassava varieties of Gunung Kidul, the highest infection was seen from Mentega variety inoculated with indigenous mycorrhiza of the Mediterranean soil of Gunung Kidul (95%). The mycorrhizal population yielded 39-98 spores/100g. Mycorrhizal diversity using indigenous mycorrhiza of Mediteran soil was higher than mycorrhiza of pandan rhizosphere and commercial inoculant, and the dominant mycorrhiza type was of spores belonging to genus Glomus. On the other hand, the indigenous mycorrhiza of Mediteran soil inoculant on various cassava varieties demonstrated similar effect as it resulted in the same number of spores, root length, and plant dry weight; despite the fact that on Kirik variety growth, the significant difference was observed on the plant height, leaf number and fresh plant weight.