The colonization of plant root cell by mycorrhizal fungi is one of the mechanisms involved for the understanding of plant bio-protection against soil-borne pathogens. The aim of current study was to investigate and describe tomato (Lycopersicon esculentum) root ultra-structural modifications caused by Glomus mosseae and the bacterial wilt Ralstonia solanacearum. In scanning electron microscopy (SEM) observations, the root cells presented several arbuscules and mature spores of G. mosseae. In transmission electron microscopy (TEM) observations, many entry points on the cell wall were detected in addition to nucleus, cell organs and many mitochondria. The results evidenced that the presence of G. mosseae can change the root architecture dramatically. R. solanacearum was inhibited by the endophytic fungi. G. mosseae structure can help the plant to prevent the pathogen bacterial invasion totally due to root architecture system changes.Key words: Mycorrhizal fungi, bacterial wilt, tomato, root cell, scanning electron microscopy, transmission electron microscopy