Understanding how evolutionary changes happen requires connecting genotype and phenotype level concepts. This study uses a form of concept map, called Knowledge Integration Map (KIM), as a learning and assessment tool to support and assess connecting concepts within and across levels. KIMs visualize clusters and cross-links by dividing the drawing area into subject-specific spaces. A technology-enhanced curriculum on evolution has been developed and implemented in four high school science classrooms (number of students n=94). Pre- and posttests consisting of multiple choice items, short essays, and concept maps triangulated changes in students’ integration of concepts related to evolution and their understanding of evolutionary changes of different organisms. Network analysis of concept maps identified changes in prominence of selected concepts and in cross-links between levels. Findings indicate that both low and high performing students made significant gains integrating concepts about the mechanisms of evolution. Results suggest that network analysis can be used to identify, compare, and track changes in concept maps over time.