The Algal Biology Toolbox Workshop Summary Report summarizes an event hosted by the U.S. Department of Energy’s Bioenergy Technologies Office’s Advanced Algal Systems Program in May 2016. The purpose of the Algal Biology Toolbox Workshop was to collect input from experts in the field of algal biology regarding (1) the current state of algal biological tools, including our understanding of algal biology and biochemistry, available molecular toolboxes, databases, and other resources; (2) challenges to developing and applying a full suite of biological tools to improve algae performance and system robustness; and (3) strategies to advance progress toward commercial algal biofuels.