Galaxea fascicularis is a hermatypic (reef-building) scleractinain coral that forms massive colonies of calcium carbonate skeleton. The ultrastructural investigations of the skeleton and the polyps of G. fascicularis that collected from the reef edge of El Ain El Sukhna (Gulf of Suez, Red Sea) have been observed by using the Scanning Electron Microscope (SEM). In this study, SEM was used to observe and understand the occurrence and distribution of microflora which may cause diseases to coral species before doing any further molecular or genomic studies. The collected colonies of G. fascicularis had green or brown colored polyps. Each polyp lives in a skeleton cup, called a corallite that had a circle of septa around the calice opening. The septa occurred in hexamerous cycles (6 primary, 6 secondary, 12 tertiary, and 24 quaternary). The deposition of two crystal types, aragonite (blade-shaped crystals) and calcite (fusiform crystals) at the growth surface of the septa were investigated. Formation of semi-solid masses by fusiform crystals suggests that the crystals might play a structural role in septal extension. Microbial communities were observed at the surface of the polyp. Fungi appeared to be a regular component of all investigated polyps, while the bacteria were observed on some polyps. The muco-polysaccharides surface of G. fascicularis might provide a matrix for microbial colonization leading to the formation of biofilm-forming microbial communities. These communities might lead to tissue degradation and holes formation.