In this article we apply a novel analytical framework to explore students' difficulties in understanding molecular genetics--a domain that is particularly challenging to learn. Our analytical framework posits that reasoning in molecular genetics entails mapping across ontologically distinct levels--an information level containing the genetic information, and a physical level containing hierarchically organized biophysical entities such as proteins, cells, tissues, etc. This mapping requires an understanding of what the genetic information specifies, and how the physical entities in the system mediate the effects of this information. We therefore examined, through interview and written assessments, 10th grade students' understandings of molecular genetics phenomena to uncover the conceptual obstacles involved in reasoning across these ontologically distinct levels. We found that students described the genetic instructions as containing information about both the structure and function of biological entities across multiple organization levels; a view that is far less constrained than the scientific understandings of the genetic information. In addition, students were often unaware of the different functions of proteins, their relationship to genes, and the role proteins have in mediating the effects of the genetic information. Students' ideas about genes and proteins hindered their ability to reason across the ontologically distinct levels of genetic phenomena, and to provide causal mechanistic explanations of how the genetic information brings about effects of a physical nature.