We develop an intelligent information system in a multilayer electronic supply chain network. Using the internet for supply chain management (SCM) is a key interest for contemporary managers and researchers. It has been realized that the internet can facilitate SCM by making real time information available and enabling collaboration between trading partners. Here, we propose a multi-agent system to analyze the performance of the elements of a supply network based on the attributes of the information flow. Each layer consists of elements which are differentiated by their performance throughout the supply network. The proposed agents measure and record the performance flow of elements considering their web interactions for a dynamic route selection. A dynamic programming approach is applied to determine the optimal route for a customer in the end-user layer.