The paper reports an ongoing research project on classroom teaching and learning involving secondary students' reasoning in genetics. Genetics is a difficult but important topic in school science yet research indicates that students do not understand genetics concepts even after instruction. Although teachers have long been using different representations in teaching science, multiple external representations (MERs) used in computer interactive multimedia (IMM) are now increasingly powerful and affordable to schools. MERs can be textual, visual-graphical, tabular, mathematical or in other formats. Researchers claim that computer-based MERs support learning by providing complementary ideas and processes, by constraining interpretations or by promoting a deeper understanding of the domain but some studies show that learners find translating between representations difficult. In this research, science teachers integrated into their classroom teaching and learning an IMM program called BioLogica that features MERs. The design of BioLogica aims at overcoming some of the linguistic and pedagogical barriers that students face when learning to understand genetics. This research uses largely qualitative methods; classroom teaching and learning with BioLogica was interpreted within a framework that includes computational and social constructivist perspectives. The research describes the benefits and costs of using MERs in developing students' reasoning in genetics.