OMAYED Biosphere Reserve (OBR) is the only biosphere on the northwestern coast of Egypt, representing the Mediterranean ecosystem. It has characteristic fauna and flora, as it comprises 12% and 17% of Egypt's flora and bryoflora, respectively, aside from the numbers of endemic and endangered animals. In the past decade, OBR was subjected to extensive human activities—the building of coastal touristic villages, irrigation canals, plantation, and some military construction—resulting in a massive decrease in its flora from 253 to 145 taxa and an increase in the number of invasive plants. This study aimed to survey the microflora and macroflora of OBR. Results recorded three new invasive flowering plants—Herniaria hemistemon, Reseda decursiva, and Trigonella corniculata—and Barbula unguiculata Hedw. and Fissidens arnoldenii R. Ruthe for the first time from the Mariotic sector of Egypt. The survey for the microflora was performed using metagenomic analysis, revealing 72 identified fungal species belonging to 10 phyla, 24 classes, 42 orders, 72 families, and 72 genera, 257 identified bacterial/archaeal species belong to 2 kingdoms, 51 phyla, 61 classes, 119 orders, and 221 families, and 490 genera identified from the plant rhizosphere. Based on the Kyoto Encyclopedia of Genes and Genomes pathway annotations, the highest number of bacterial species was counted for membrane transport pathways, carbohydrates, and amino acid metabolism, reflecting the abundance of symbiotic and beneficial microbiota. The most abundant fungi found associated in the plant rhizosphere were mostly pathotrophs-symbiotrophs.