The growing international trade needs a logistic system managing the transportation system to create continuity in its process. Indonesia, as a country having land borders with neighboring countries, needs research about the freight transportation system with those different characteristics. Meanwhile, there is a tendency where the shift of the freight model paradigm results in the movement of the aggregate analysis approach to disaggregate or agent-based approach. With the need to consider the role and influence of actors' decisions in the analysis-based of freight transportation, the agent-based model will become will be a supporting tool to analyze freight transportation. This paper will identify and elaborate on the actors or stakeholders having roles in the freight transportation system in cross borders, mainly the marine product commodities. To determine the most significantly influential stakeholders in the analysis of freight transportation in the cross-border area, we used the analytical network process (ANP) method. ANP is the improvement of AHP Analytical Hierarchical Process (AHP) by referring to the thoughts that there is a correlation in the network form between elements where ANP enables the occurrences of inner dependence within a set (clusters) of elements and outer dependence among different sets (clusters). Based on the analysis using ANP, we found that the company owners are the most influential party followed by governments, employees, and customers. The link of result of stakeholder mapping and the relationship patterns among stakeholders, and it gives a strong foundation in the agent-based model needed in contemporary freight transportation modeling.