In recent years, an increase of research on microalgae have been seen due its promising potential as an alternative feedstock for biofuel. It offers high oil yield per land area compared to the first and second generation biofuel feedstock. Given the tropical climate and the archipelagic structure of the Philippine islands, it provides a thriving habitat for more than a thousand species of microalgae. Hence, abundance of microalgae species are found in the country. However, the archipelagic structure of the country also may come as a disadvantage as the transportation of biofuels may require varying shipping routes. In life-cycle assessment of biofuels, transportation is one of the sources of environmental emissions. Thus, minimizing the distance travelled by the ship can dramatically reduce the energy usage and environmental impact of the transportation process. This study proposes an ant colony optimization (ACO) method in determining the optimal route between the different ports in the Philippines. The results in the study showed that the choice of vehicle used has significant impacts on the total shipping distance travelled. This study can be further expanded with the inclusion of time windows.