The rapid pace of genomic discovery has raised public expectation and concerns about the utility of new discoveries and their potential to exacerbate health disparities. Improving literacy concerning gene and environmental (GxE) contributors to disease is needed to avoid commonly observed deterministic misconceptions about genomics. Mental models approaches that incorporate community engagement processes could be used to inform GxE literacy-building interventions. We used a mental models approach to describe and systematically compare expert and lay understanding of GxE interactions, using the example of podoconiosis, a non-infectious lymphedema endemic in highland Ethiopia. Methods included: (1) specifying elicitation questions for a literature review, (2) eliciting an expert model, (3) eliciting a lay model, and (4) comparing the two models. We used a coding scheme to identify lay participants' knowledge gaps, misunderstandings and extra knowledge relative to the expert standard. Results indicated that lay participants' viewed poverty as an important susceptibility factor and considered heredity and contagion to have a joint causal influence. Experts did not endorse either of these viewpoints. Conventional expert-based interventions aimed to correct misconceptions about behaviors important for prevention may be stymied by lay views that social environmental factors have more important influences on health outcomes. GxE literacy interventions that consider multiple levels of influence including social determinants of health and personal resilience to augment health education strategies are needed in diverse settings. Novel communication approaches will be needed to help target audiences disentangle long-held conceptions of heredity and contagion.