Part of the struggle learners face when confronting concepts in molecular genetics comes from the very nature of molecular cell biology (MCB) knowledge itself. Molecular mechanisms rely on multi-level reasoning, which is very difficult for beginners. Concepts and processes of MCB are “un-seeable” and rely on the ability to create and correctly interpret visual representations. Undergraduate students must develop skills of visual literacy, but to date there is no unified framework that describes common visual representations of MCB. We developed a 3x3 matrix, “the DNA Landscape,” based on examination of diagrams in undergraduate textbooks. The DNA Landscape is both a research and teaching tool that recognizes two dimensions of representations for any diagram involving DNA: scale (nucleotide through chromosomal levels) and abstraction (how closely it resembles the actual shape of the molecule). We tested the robustness of the Matrix by coding >2000 figures from 12 textbooks. Many figures contained multiple representations, but all were able to be coded using this new framework. Different MCB topics tended to use specific types of representations. For example, Mendelian genetics uses allele names, scale maps, and chromosomes quite often, but gene expression tends toward box and line structures and chromatin “string.” Preliminary results suggest that experts move easily around the landscape, but students have difficulty making connections between different representations of the same phenomena. To help learners develop an integrated knowledge base, educators need to go beyond assessing individual points within the matrix and instead teach and assess the connections between points.