The present production of biofuels has a high cost when compared against fossil fuels. The crucial part in this process is cellulose hydrolysis, because the enzyme systems that are presently used in the market are too expensive. Our goal is to develop new enzyme systems that have enhanced celluase activity relative to the commercial cellulase systems that are presently used. Using the protein sequences of cellobiohydrolases and endoglucanases from T.reesei as well as betra-glucosidase from A. niger, we searched 13 different fungal genomes. We identifed more than 200 candidate genes that we are currently cloning and expressing in A. niger. The heterolgous genes that can be functionally expressed in A. niger are biochemically characterized and subjected to pair wise comparison with commercially available cellulase system enzymes. We present here an overview of the results we have obtained to date and a detailed characterization of three endoglucanases, two from glycosyl hydrolase family 5 and one from family 12.