Synthetic biology is an interdisciplinary field that brings together biology and engineering at its core. Understanding and evaluating the ecological effects of synthetic biology applications also require broad interdisciplinary convergence and the ability to adapt to rapid technological developments. This article describes a series of workshops designed to provide a space for interdisciplinary groups of synthetic biologists, natural and social scientists, and other stakeholders to identify priority ecological hazards and to begin to design research programs to inform ecological risk assessments and risk management of synthetic biology applications. Participants identified gene flow, fitness, and competition as the key hazards of synthetic biology applications using engineered microorganisms. The rapid pace of synthetic biology research and product development, the potential environmental release of numerous applications, and the diffuse and diverse nature of the research community are prompting renewed attention on how to design robust ecological risk research programs to investigate such hazards.