Filamentous fungi are used for the commercial production of various metabolites. Early strain development programs involved the improvement of product yield by random mutagenesis and screening and protoplast fusion. Currently, molecular techniques such as genetic transformation and protein engineering are being applied for the further refinement of fungal products and production systems. As eukaryotic microorganisms capable of post- translational modification of gene products and of secreting them into the culture medium, filamentous fungi are attractive hosts for products of high value or volume. Functional genomics and the emerging proteome studies will generate an invaluable information base paving the way for a holistic approach in fungal strain improvement.