Ethanol from renewable resources has been of interest in recent decades as an alternative fuel or oxygenated additive to current fossil fuels. Bioethanol can be produced by fermentation from a variety of raw materials which contain sugars, starch and lignocellulosic substances. A great number of fungi are able to produce ethanol. Zygomycetes are saprophytic filamentous fungi, which are able to produce several metabolites including ethanol. Among the filamentous fungi Mucor indicus (formerly M. rouxii ) showed good performances on ethanol productivity from glucose, xylose and wood hydrolyzate. M. indicus has been shown dimorphism properties. It is able to grow either in yeast like or filamentous forms. Beside the production of ethanol the biomass of this fungus contains appreciated level of chitosan which is a valuable product. In the current study, we studied the ability of the different morphology of M. indicus for ethanol production under aerobic and anaerobic condition from glucose, fructose, sucrose, sugarcane molasses and sugar beet molasses. This fungus showed the ability to produce ethanol from glucose and fructose, but it can not ferment sucrose. Therefore, we examined the fermentation of enzymatic inverted sucrose and the molasses. The yield of production of ethanol, glycerol, biomass and chitosan on glucose, fructose, sugarcane molasses, sugar beet molasses, inverted sucrose, inverted sugarcane molasses and inverted sugar beet molasses were examined. The maximum yield of ethanol and glycerol were obtained under anaerobic condition and the maximum yield of biomass was obtained under aerobic condition, where as the yield of ethanol from yeast like morphology is the same as mycelial morphology and the yield of biomass of yeast like is more than mycelia. On the other hand the yield of chitosan obtained from mycelia is more than yeast like. The sugarcane and sugar beet molasses and their sucrose inverted form are good sources for biomass and chitosan production, where as the enzymatic sucrose inverted sugarcane and sugar beet molasses are good alternative for production of ethanol.