Historically, natural products have been used for the treatment of many diseases since ancient times. One of the earliest records of medicinal use of natural products dating back to the ancient Egyptian civilization (pharaohs). As an Egyptian pharmaceutical record, the ancient Egyptian medical Ebers Papyrus (2900 B.C.), in which over 700 plant-based drugs were recorded for the treatment of many diseases. In our days, great attention has been given to endophytic fungi due to the chemical diversity of their secondary metabolites. Therefore, this study was undertaken to isolate and identify endophytic and associated fungi from plant and marine organisms collected from two locations in Egypt, Hurghada and Inland saline lakes of Wadi El Natrun. As a result 51 pure fungal strains were isolated, cultivated on different media and their extracts were screened biologically as antimicrobial against some pathogenic microorganism and as antioxidant activity using DPPH. Based on the bioassay data, 15 isolates were exhibited interesting antimicrobial and antioxidant activity. Morphological and genetic studies of the selected isolates have shown that, they are belonging to six genera (Aspergillus, Epicoccum, Penicillium, Cladosporium, Paecilomyces, Alternaria). Based on chemical screening and derelictions by analysis of the LC-MS/MS and H1 NMR data, the extracts with promising chemical profile were purified using different chromatographic techniques and pure compounds were evaluated as antimicrobial, antibiofilm against some clinical pathogens. Our main target is to use these bioactive compounds to functionalize the textile to improve comfort, performance and protection properties of fabric include antimicrobial, UV-Protection, self-cleaning and odor control.