In the last 40 years, several scientific and technological advances in microbiology of the fermentation have greatly contributed to evolution of the ethanol industry in Brazil. These contributions have increased our view and comprehension about fermentations in the first and, more recently, second-generation ethanol. Nowadays, new technologies are available to produce ethanol from sugarcane, corn and other feedstocks, reducing the off-season period. Better control of fermentation conditions can reduce the stress conditions for yeast cells and contamination by bacteria and wild yeasts. There are great research opportunities in production processes of the first-generation ethanol regarding high-value added products, cost reduction and selection of new industrial yeast strains that are more robust and customized for each distillery. New technologies have also focused on the reduction of vinasse volumes by increasing the ethanol concentrations in wine during fermentation. Moreover, conversion of sugarcane biomass into fermentable sugars for second-generation ethanol production is a promising alternative to meet future demands of biofuel production in the country. However, building a bridge between science and industry requires investments in research, development and transfer of new technologies to the industry as well as specialized personnel to deal with new technological challenges.