The usage of sustainable energy sources is in accordance to the global strategy of sustainable development. The usage of biofuels in transport increases the safety of supply and reduces the dependence of the traffic sector on oil, reduction of greenhouse gas emission from the road transport, and support of the sustainable development of rural areas. Biofuel advantages (biodiesel and bioethanol) in relation to other alternative fuels can be seen in the usage of the existing vehicles with no or relatively slight modifications of existing vehicles, which depends on the concentration of biofuels in blend with fossil fuel. Biofuel as a sustainable energy source are a particular importance for Croatia because it can replace fossile fuels for transport which accounted more than 30 percent in total energy consumption, with a constant tendency of growth and these are significant source of greenhouse gas emissions. The basic principles of strategy in Croatia are: certainty of energy supply, competitiveness of the energy system and the sustainability of energy development, competitiveness of the energy system and the sustainability of energy development. The aim of modeling and analyzing 100% independent energy system is to make the system sustainable and to ensure adequate certainty of energy supply and independence.