The phyla Ascomycota and Basidiomycota belong to the kingdom of fungi, including filamentous and unicellular organisms. Aspergillus species, which belong to the phylum Ascomycota, are saprophyte ubiquitous filamentous fungi found in soil, water and any decaying material. They are known to produce natural compounds which are both beneficial and deleterious to mankind. Morphogenesis and secondary metabolite production in Aspergillus species is a complex puzzle, yet to be solved. Genes involved in morphology of the fungus are known to be genetically linked and influence regulatory mechanisms controlling secondary metabolite production in the model fungus Aspergillus nidulans . In Aspergillus and other fungal genera, genes responsible for secondary metabolite production are normally found clustered. Identification of such gene clusters and of the regulatory genes that control them will aid in the discovery and production of novel secondary metabolites with possible benefits.Another interesting genetic regulatory mechanism described in fungi is the osmotic stress response pathway that allows these organisms to survive extreme conditions. Among the fungal species most resistant to high osmotic stress is Wallemia sebi , which belongs to the phylum Basidiomycota. This xerophilic mold is capable of growing in dry conditions (i.e., low water activity) and is commonly isolated from jams, dates, bread, cakes, salted beans, fish, bacon, fruits, soil, hay, and textiles. The ability to adapt and survive in highly saline environment has generated interest among researchers to investigate the genetic potential of this organism.This thesis includes the study several genetic regulatory mechanisms in fungi: (1) role of the transcription factors CrzA and SltA in morphogenesis and sterigmatocystin toxin production in Aspergillus nidulans , (2) in silico analysis of novel gene clusters, numbered 27 and 39, involved in secondary metabolite production in Aspergillus flavus and (3) in silico analyses of osmotic stress response genes in Wallemia sebi .