Ensuring a secure, stable and affordable supply of liquid fuels for the transport sector has emerged as a key concern of many governments worldwide. To identify the efficient portfolios of fuel supply available to a country, the security of available fuel supply options must be balanced against the cost of those fuels. This study first demonstrates the use of mean-variance portfolio theory approaches to identify the optimal transport fuel supply for the United States and Japan in the present day. We then construct a transport fuel security index (TFSI) to assess the security of potential fuel sources, such as crude oil and biofuels, by including indicators for diversity of supply and geopolitical risk. For comparison with the mean-variance approach, the TFSI is used as a measure of risk for identifying optimal fuel supply portfolios in the present day for the USA and Japan. According to both the mean- variance and TFSI approaches, we find that the existing fuel mixes of the USA and Japan do not lie within the efficient set of available fuel supply portfolios. We then apply the TFSI to various scenarios for the year 2030, based on current fossil fuel projections and techno- economic evaluations of emerging algal biofuel technologies, to identify a set of efficient fuel portfolios for 2030. Our results show that advances in biofuel technology have the potential to improve both the affordability and accessibility of the fuel supply in 2030, and that this contribution is dependent on both the level of algal technological development and the price of crude oil in the future.