Filamentous fungi are remarkable organisms that are naturally specialized in deconstructing plant biomass. This feature explains their tremendous potential for biofuel production from renewable sources. However, organisms from this group need to be engineered to make them compatible with standard operating procedures of the industry and to optimize their applications in the field of biotechnology. Here, we discuss the development of new tools and approaches for the engineering of fungi for biotech applications such as the production of biofuels. These tools include not only next-generation “omics” tools to obtain deeper insight into the molecular biology of filamentous fungi, but also novel engineering approaches for the genetic modification of these organisms to generate highly efficient cell factories. The first set of tools, in framework of Systems Biology, targets understanding how these fascinating organisms are able to integrate multi-level environmental information in order to coordinate gene expression and protein production in response to changing conditions. The second approach, in the context of Synthetic Biology, provides physical and conceptual tools that allow the genetic modification of fungi, mainly through the construction of synthetic promoters for the expression of heterologous genes in these organisms and either expanding their capabilities or reshaping their regulatory networks. Finally, we discuss some new directions that have been initiated or should be addressed in future work in order to fill gaps still existing in the field.