Zygomycetes are a large and wide-spread group of filamentous fungi. Many species have great use e.g. as tempeh which is a popular food in Southeast Asia. These fungi are primarily saprophytic, capable of assimilating lignocelluloses and agricultural waste materials and producing a variety of metabolites. Since 1999, we have studied physiology and metabolite formation of more than 100 strains of zygomycetes from Rhizopus, Mucor and Rhizomucor genera. The growth of these fungi were investigated on spent sulfite liquor, lignocellulosic hydrolyzates, rice straw, orange peels, etc. These fungi are generally able to take up hexoses and pentoses, and even dimers such as cellobiose. Mucor sp. such as Mucor indicus are superior to baker’s yeast in terms of ethanol yield and productivity. We approach an integrated application of zygomycetes, where they are cultivated on lignocellulosic materials for ethanol production. The biomass of the fungi will then be used as fish feed or further processed to produce biological superabsorbents, which can be converted to biogas at the end of its lifetime. It means zygomycetes-based biorefinery produces several products simultaneously, which makes ethanol process more feasible. In this work, a summary of 12 years research on zygomycetes will be presented.