A two-level Factorial Design study was done for the purpose of making a direct statistical comparison of the performance of high test molasses (HTM) and blackstrap molasses (BM) as fermentation substrates. The dependent variables under study were alcohol yield and congener formation for 24-hour fermentation. Another purpose was to identify those independent variables (and the interactions of those variables) which have significant effects over the dependent variables under study. The independent variables were fermentation substrate, initial yeast cell count, molasses feed addition time and quantity of molasses feed added. Sixteen pilot plant scale (3785 L) fed batch fermentations were performed. Variables which showed a statistically significant (p = 0.05) effect on alcohol yield and congener generation were fermentation substrate and quantity of molasses feed added. A significant effect of fermentation substrate on pH and total acidity was also observed. In general BM fermentations were in a more advanced stage and produced higher fusel content than HTM fermentations at 24 hr of fermentation.