This study attempts to develop a method for identifying "bottleneck" stations on the inter-regional public transport network. Investing in these bottleneck stations enables the network to be more convenient. First, a method for identifying bottleneck stations on the network was formulated based on multi-objective optimization with a generic algorithm. Second, a system was developed to automatically identify bottleneck stations in a manner which makes them visible. A network outlining the actual inter-regional network in Japan was constructed. The results of numerical experiments on this network suggest that bottleneck stations may be located not only in the metropolitan areas but also in principal cities in the countryside.