Another promising lipids source, still not implemented but currently being studied worldwide, is represented by microalgae. Microalgae have a high potential as biodiesel precursors because many of them are very rich in oils, sometimes with oil contents over 80% of their dry weight, although not all species are suitable as biodiesel production oils (Chisti, 2008; Manzanera, 2011). Besides, these microorganisms are able to double their biomass in less than 24 hours, achieving a reduction between 49 and 132 fold in the medium culture time required by a rapeseed or soybean field. Furthermore, microalgae cultures require low maintenance and can grow in wastewaters, non-potable water or water unsuitable for agriculture, as well as in seawater (Mata et al., 2010). The production of microalgae biodiesel could be combined with the CO2 removal from power generation facilities (Benemann, 1997), the treatment of waste water from which microalgae would remove NH4+, NO3- and PO43- (Aslan & Kapdan, 2006), or the synthesis of several valuable products, from bioethanol or biohydrogen to organic chemicals and food supplements (Banerjee et al., 2002; Chisti, 2007; Rupprecht, 2009; Harun et al., 2010). However, microalgae biomass-based biofuels have several problems ranging from the optimization of high density and large surface units of production to the location of the microalgae production unit. Anyway, the main decisions to take are the adoption of open or closed systems, and the election of batch or continuous operation mode. As will be discussed below, depending on the system and mode of operation choice, there will be different advantages and drawbacks.