In recent years, widespread efforts have been directed towards decreasing the costs associated with microalgae culture systems for the production of biofuels. In this study, a simple and inexpensive strategy to bio-prospect and cultivate mixed indigenous chlorophytes with a high carbohydrate content for biomethane and biohydrogen production was developed. Mixed microalgae were collected from four different water-bodies in Queretaro, Mexico, and were grown in Bold's basal mineral medium and secondary effluent from a wastewater treatment plant using inexpensive photo-bioreactors. The results showed large fluctuations in microalgal genera diversity based on different culture media and nitrogen sources. In secondary effluent, Golenkinia sp. and Scenedesmus sp. proliferated. The carbohydrate content, for secondary effluent, varied between 12% and 57%, and the highest volumetric and areal productivity were 61 mg L-1 d(-1) and 4.6 g m(-2) d(-1), respectively. These results indicate that mixed microalgae are a good feedstock for biomethane and biohydrogen production. (c) 2014 Elsevier Ltd. All rights reserved.