Biodiesel was produced by direct esterification of Cunninghamella echinulata dry mass using sugarcane molasses as substrate in the first stage of fermentation. GC/MS results for fatty acid methyl esters revealed abundant low degree unsaturated long chain fatty acids and saturated long chain fatty acids that are similar to plant oils. In the second stage, the spent medium of C. echinulata culture was used as the fermentation medium for hydrogen production by Clostridium acetobutylicum ATCC 824. The maximum total H2 yield was 1450 ml H2/l after 48 hr fermentation. In the third stage, the spent medium of Clostridium containing volatile organic acids was used for methane production by methanogenic bacteria. The highest cumulative methane yield was 1690 ml l-1 spent medium obtained after 48 hr. The gross energy content of biodesel, H2 and methane generated through three successive stages fermentation from 84 g molasses was 3928 kJ mole-1. The results presented in this study suggest a possibility of interlinking biodiesel production technology by fungi with hydrogen production by C. acetobutylicum and methane production by methanogenic bacteria to exploit the residual sugars and organic acids in the spent medium and therefore increase the economic feasibility of the bioenergy production from molasses.