Microalgae are promising platforms for producing diverse biocompounds relevant to multiple commercial sectors, and the use of genomic technologies in microalgae is rapidly expanding. To examine the research trends, we conducted a bibliographic analysis (systematic map) of this rapidly developing field. Our study presents a descriptive overview of genomic techniques in microalgae for industrial applications, highlighting emerging trends and key knowledge gaps. After the initial identification of more than 23,600 scientific publications, we screened over 5,500 original research studies that were deemed most relevant by AI-based sorting. We then selected 518 relevant studies in which microalgal strains were genetically modified to improve traits of commercial interest. We also compiled information on industrially relevant sectors that potentially benefit from genetically improved microalgae. Overall, more than 60 strains from 10 genera, mainly belonging to green microalgae, cyanobacteria and diatoms, were genetically improved for future commercial applications. Most studies used conventional genetic engineering techniques, with incipient research on gene editing tools. The most frequently improved microalgal traits varied with the type of cell (eukaryotic microalgae vs. cyanobacteria). Genetically improved eukaryotes (mainly green microalgae) produced proteins, lipids and pigments, while cyanobacteria synthetized alcohols, polyols and terpenoids. The main recipient of the improved strains is the human health sector, followed by the bioenergy sector, food and beverage industries, animal farming including aquatic animals, and cosmetics. Manufacturers of bioplastic packaging, chemical industries, environmental remediation companies, wastewater treatment plants, and the agriculture sector may also benefit from the use of genetically improved microalgae and their derived products.