Microalgae such as Nannochloropsis and Chlorella are attractive sources of biomass for food, feed, and industrial applications. For a long time, their use in biotechnology was limited by a lack of molecular tools. This is now beginning to change: while transfection and gene-editing methods are still developing, the growing availability of genome sequences is laying the foundation to start exploring targeted gene editing to better understand and improve these species for biotechnological use.