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Nutritional value, crop yield, food quality, shelf life and safety can be enhanced by gene editing technologies in agriculture and food industry. Genome editing techniques are useful for manipulating genes, investigating their functions in biology and improving traits for genetic engineering in biotechnology. Genome editing has been facilitated by engineered nucleases, which are dubbed molecular scissors, including zinc finger nuclease (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced palindromic sequences (CRISPR/Cas9). Among these nucleases, CRISPR/Cas9 has vividly increased its applications for genome editing in the past 6 years with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in various organisms like microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feed stocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.