This article examines conceptual learning of genetics in a Year 10 Australian classroom from an ontological perspective. The study was part of a larger research project about teaching and learning genetics with computer-based multiple representations. Genetics is an important but difficult topic to teach and learn at school. The study used an interpretive research approach with a case-study design. Over six weeks, the science teacher taught genetics and engaged his students in computing activities of BioLogica, an interactive program that features multiple representations. Data were collected from multiple sources including classroom observations, interviews and online tests. Data analyses and interpretations indicated that gene conceptions of most students were not sophisticated and that they did not have radical conceptual change that involves a shift across the ontological categories of matter and processes. The findings were largely consistent with students' prior knowledge and the teacher's teaching. The authors highlight the role of the classroom teacher and the use of multiple representations in fostering ontological conceptual change and suggest some directions for further research.