Fungi microbiomes can be studied using a several approaches. Most entail using chemical dyes to stain typical morphological traits, which can be hazardous to both the environment and the health of users. In order to use safe alternative dyes for fungi microorganisms' studies, the objective of the present work was to find new alternative dyes that would help us study the biodiversity of root microbiomes in their natural biofilm. Roots of seven different species were harvested: Poa spp., Genista aspalatoid, Cistus libanotis, Thymelaea tartonraira, Juniperus oxycedrus, Cupressus dupreziana, and Pinus halpensis. Following blanching the roots using a modified Philips and Hayman's (1970) procedure, we stained the various endophytic microbiome structures with black mulberry dye and compare this dye's effectiveness to that of two types dyes; natural and synthetic (Curcuma and methylene blue). Results revealed that the best staining was obtained with Black mulberry, the roots' species' endophytic fungal structures were transparent and stained with a brown sparkle hue. The rate of colonization of these fungi is very high in the herbaceous species. A new shape of sporangium was found in the T. tartonraira specie. This procedure of staining is successful, effective and offers safer alternatives to the harmful chemical's dyes used in traditional staining methods.