Overexpressing recombinant fungal proteins has been a considerable challenge for the past few years. We describe here an Aspergillus niger fusion-protein expression system which allows the secretion of recombinant proteins. For this study, we selected 46 Aspergillus niger genes of different functions to be cloned in two different expression vectors. The system uses the Phanerochaete chrysosporium mannanase A signal peptide and cellulose-binding domain. The signal peptide is involved in fusion protein secretion whereas the cellulose-binding domain was intended to facilitate protein purification using cellulose magnetic beads. The cellulose-binding domain was also expected to increase the level of enzyme activity but the results were not conclusive. Another purpose of this project was to set up rapid and low-cost medium or high throughput methods for cloning, expression and enzymatic screening for several type of enzymes in parallel. Using these methods, we were able to obtain a 95% success rate for cloning and a 50 to 60% success rate for expression.