The aquatic plants are a promising renewable energy resource. Lake Fúquene polluting macrophytes, water hyacinth (Eichhornia crassipes C. Mart.) and Brazilian elodea (Egeria densa Planch.), were saccharifiedby different treatments and fermented to ethanol by native yeasts. Among the tested chemical and biological methods for the saccharification, Pleurotus ostreatus at 10% (m/v) was chosen as the best pre-treatment in both macrophytes (P<0.01). Subsequently 49 yeasts were isolated from Lake Fúquene and nine strains were selected, which presented the highest precipitates characteristic of ethanol in the iodoform test. The fermentations from water hyacinth and Brazilian elodea hydrolysates using these yeasts produced ethanol at a rate between 0.38 to 0.80gL-1h-1 and 0.15 to 0.27gL-1h-1 respectively. The ethanol presence was confirmed by gas chromatography–mass spectrometry. The nine yeasts chosen were preliminarily identified as belonging to the genera Candida spp., Brettanomyces sp. and Hansenula spp.