The paper is devoted to the knowledge assessment system that has been developed at the Department of Systems Theory and Design of Riga Technical Uni- versity for the last four years. The system is based on concept maps that allow displaying the knowledge structure of a particular learner in the form of a graph. Teacher’s created concept maps serve as a standard against which learner’s concept maps are compared. However, it is not correct to compare teacher’s and learners’ con- cept maps by examining the exact equivalence of relationships in both maps, because people construct knowledge in different ways. Thus, an appropriate mechanism is needed for the flexible evaluation of learners’ concept maps. The paper describes the algorithm implemented in the concept map based knowledge assessment system and its evolution through four prototypes of the system.