The fermentation step is central in the overall fuel ethanol production process since it represents the actual transformation of the conditioned and pretreated raw materials into the main product, ethyl alcohol, using bioagents such as yeast or other ethanol-producing microorganism. Ethanolic fermentation is one of the most studied biological processes. Nevertheless, the need of increasing the effi­ciency of ethanol production including the usage of alternative feedstocks has led to the development of new fermentation methods with better technoeconomic and environmental indicators.

Traditionally, the most used microorganism for ethanolic fermentation is the yeast Saccharomyces cerevisiae. This is valid for practically every one of the main types of feedstocks employed for ethanol production: sucrose-based media, starchy materials, and even lignocellulosic materials. However, in the last case, there is a wider variety of process microorganisms employed (e. g., Zymomonas bacteria, xylose-assimilating yeasts, or thermophilic clostridia).