Abstract: Microflora including bacteria, actinomycetes, yeasts and filamentous fungi recovered from the leaves of Juniperus procera collected from two different altitudes at January and July 2007 from Aseer region, Saudi Arabia. Types and numbers of microflora varied according to the altitude and the month of collection. The number of microflora was higher on old leaves than young ones in most cases. Low altitude exhibited more microflora than high altitude. The relationship between meteorological factors and type and number of the recovered microflora was investigated. Inoculation of detached healthy leaves of Juniperus procera by predominant fungal isolates revealed that only Alternaria alternata as a pathogen of this plant. To confirm the pathogenicity of this fungus, scanning and transmission electron microscopic examination revealed the colonization of this pathogen inside the leaf tissue. Penetration of Juniperus leaves by the fungus occurred only through stomata and the invading hyphae were located in the intercellular spaces of leaf tissues. Bacteria also observed inside the intercellular spaces of leaf tissues of the host plant and not inside the leaf cells. Adjacent host cells to bacteria were also affected. Ultrastructural changes in the infected cells, from inoculated leaves, included changes in chloroplasts, nuclei and mitochondria.