Fungi have been an important source of many structurally diverse and biologically active secondary natural products. These secondary metabolites have found applications in pharmaceutical and agriculture industry. Fungi are estimated to be second only to insects in species diversity. It is estimated that there are at least 3.5 million species of fungi of which a less than 5% have so far been explored. Fungi are known to produce many secondary natural metabolites, however their role has still not been clearly understood. However it is possible that fungi which often thrive in competitive environments would experience evolutionary pressure to produce such metabolites for defensive or offensive functions. Our research focusses on isolation and structure elucidation of secondary metabolites from endophytic and mycoparasitic/fungicolous fungi. Mycoparasitic and fungicolous fungi are those that colonize other fungi, and could be potential sources of antifungal agents because of the negative effects exerted on their hosts due to this colonization. Endophytic fungi are those that colonize the inner tissues of plants in a symbiotic or a non-symbiotic manner. They may or may not be necessary for the growth, defense and survival of the host. They may protect the plants from attack by other pathogens by producing secondary metabolites that inhibit the growth of other pathogenic organisms. Many biologically active secondary metabolites have been isolated from various members of these two classes of fungi. During the course of this research fourteen new and several known compounds representing various biosynthetic classes including peptides, polyketides, terpenoids, and compounds with mixed biogenetic origins have been isolated and characterized using various tools such as NMR and MS. Details of the isolation, structure elucidation, and biological activity of these new compounds are presented in this thesis. Structure elucidation was performed mainly by analysis of various MS and NMR data, along with chemical derivatization reactions and/or X-ray diffraction analysis data. Absolute configuration assignments were made using, X-ray crystallography, and/or by ECD spectral analysis in combination with computational analysis.