For the discovery of new therapeutic candidates, natural products continue to play an important role. Over the past 3 decades, natural products or their derivatives have been reported to produce about 60% of new anticancer agents and almost 75% of all new antimicrobial molecules which account for antibacterial, antifungal, antiprotozoal and antiviral molecules. More than a hundred natural products and natural product-derived substances were being evaluated in clinical trials or were being registered at the end of 2015. Bioactive or secondary metabolites have been isolated from a variety of terrestrial and marine organisms, including plants, marine invertebrates and microorganisms. Microorganisms (traditionally bacteria and filamentous fungi, but the recent advances include cyanobacteria, microalgae and myxobacteria) are one of the most prevalent sources for the production of bioactive molecules. Exploitation of their specialized (or secondary) metabolism has guaranteed for decades the discovery of novel antibiotics and other compounds with unprecedented chemical characteristics and biological properties not existing in screening. The current study is based on isolation and exploitation of the secondary metabolism of such fungal strains that prove potential source of such bioactive molecules and also for pharmaceutical drug discovery programs.