Microalgae are promising sources of biofuels due to the high lipid content of some species. However, growing microalgae at large scales involves high production costs, mainly associated with nutrient inputs and harvesting processes. Therefore, to be cost competitive, species to be used as a source of fuels should be capable of accumulating lipids and biomass at lower fertilizer inputs. In the present study, we isolated and identified a native microalgal strain of Botryococcus sp. which was cultured under varying nitrogen, phosphorus and carbon dioxide regimes. The effects of nutrient availability on biomass, lipid production and fatty acid profiles were examined. We observed an increase in the relative lipid content from 25.5% under nitrogen non-limiting conditions to 41.8% under nitrogen deprivation. The lipid profile induced by nitrogen limitation was found to be dominated by saturated and monounsaturated lipid classes, meeting the European Standards for biodiesel and oil suitable for biofuel production. Thus, this Botryococcus sp. has the potential to be used at large scale cultures with the purpose of producing biofuels with lower fertilizer costs.