Microalgae are considered to be the feedstock for third‐generation biofuels but there are still no commercial applications of microalgae biomass. This is due to the costly harvesting process, resulting from their specific characteristics such as small cell sizes, negatively charged surfaces, and stable dispersion in culture broths. Chitosan derived from crustacean shells, as a highly efficient and non‐toxic flocculant for the harvesting of microalgae, can simultaneously achieve value‐added recycling of shell wastes and efficient flocculation of microalgal biomass. Shell‐derived chitosan is a biopolymer with a high economic value, which might promote shell waste resource utilization. Its application for microalgae harvesting also has no effect on the downstream process for biodiesel production. More than 90% of microalgal biomass can be harvested under certain conditions using chitosan as the flocculant, demonstrating a strong potential for practical application in future. The application of chitosan to flocculate microalgae still has some limitations, and efforts should be made regarding the enhancement of cost‐effectiveness, improvement of harvesting processes, scalability of practical application, and implementation of supporting policies. The contribution of this study lies in the combination of chitosan production from crustacean shell wastes and its application in microalgae harvesting, which can realize the value‐added recycling of shell wastes and efficient flocculation of microalgal biomass. © 2021 Society of Industrial Chemistry and John Wiley & Sons Ltd