Algae are diverse organisms with significant biotechnological potential for resource circularity. Inspired by fermentative microbes, engineering algal genomes holds promise to expand their applications. Advances in genome sequencing, DNA synthesis, and delivery techniques enable customized molecular tools to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes in heterotrophic prokaryotes and eukaryotic microbes could also apply to photosynthetic algae. Future algal genome engineering will enhance yields of native products and enable expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. This review presents a historical perspective on advances in engineering algae, discusses genetic traits needed for genome optimization, draws inspiration from whole-genome engineering in other microbes, and presents candidate algal species for these goals. Algae are a diverse group of organisms, ranging from large multicellular species resembling plants to simple unicellular protists. Despite shared ancestral origins, algae exhibit ecological, genetic, and physiological diversity exceeding that of most other taxa. Algae have plastids containing remnant genomes from a singular primary endosymbiotic event involving a cyanobacterium. Most algae retain the capacity for photosynthesis. Three main groups of algae arose after the initial endosymbiotic event and served as the foundation for dominant photosynthetic eukaryotes, including land plants. Algae can be used in biotechnology for bioconversion of low-value inputs into biomass and higher-value bioproducts. Photosynthetic algal cultures require minimal chemical inputs compared to fermentative organisms, and many algae thrive under mixotrophic conditions, making them ideal for upcycling complex wastewaters. Algal biotechnology focuses on unicellular or multicellular microbial species cultivated in photobioreactors or open pond systems. Enclosed systems offer superior control over culture conditions but are more expensive than open systems. Algae can be cultivated on non-arable land using brackish or salt water and have higher theoretical productivity in biomass per unit time than traditional land crops. Genetic engineering of algal genomes provides opportunities to add additional value to their cultivation. The promise of algal biotechnology lies in using photosynthetic microbes to grow in wastewater using solar energy to capture nutrients that would otherwise be discarded and convert them into specific chemicals of interest. Algal cells' organellar compartmentalization provides a platform for producing non-glycosylated recombinant proteins in the chloroplast or glycosylation of proteins in the endoplasmic reticulum (ER) and subsequent secretion. Algal cells may also be favorable eukaryotic environments for metabolic engineering approaches to produce specialty metabolites by expressing vascular plant enzymes. However, several barriers hinder the broad implementation of algal species as host cell systems for molecular engineering. Photosynthetic growth, while advantageous from a sustainability perspective, also requires infrastructure considerations to ensure adequate light penetration and carbon dioxide supply into cultivation vessels, factors that generally yield lower volumetric cell densities than fermentation. NeverthelessAlgae are diverse organisms with significant biotechnological potential for resource circularity. Inspired by fermentative microbes, engineering algal genomes holds promise to expand their applications. Advances in genome sequencing, DNA synthesis, and delivery techniques enable customized molecular tools to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes in heterotrophic prokaryotes and eukaryotic microbes could also apply to photosynthetic algae. Future algal genome engineering will enhance yields of native products and enable expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. This review presents a historical perspective on advances in engineering algae, discusses genetic traits needed for genome optimization, draws inspiration from whole-genome engineering in other microbes, and presents candidate algal species for these goals. Algae are a diverse group of organisms, ranging from large multicellular species resembling plants to simple unicellular protists. Despite shared ancestral origins, algae exhibit ecological, genetic, and physiological diversity exceeding that of most other taxa. Algae have plastids containing remnant genomes from a singular primary endosymbiotic event involving a cyanobacterium. Most algae retain the capacity for photosynthesis. Three main groups of algae arose after the initial endosymbiotic event and served as the foundation for dominant photosynthetic eukaryotes, including land plants. Algae can be used in biotechnology for bioconversion of low-value inputs into biomass and higher-value bioproducts. Photosynthetic algal cultures require minimal chemical inputs compared to fermentative organisms, and many algae thrive under mixotrophic conditions, making them ideal for upcycling complex wastewaters. Algal biotechnology focuses on unicellular or multicellular microbial species cultivated in photobioreactors or open pond systems. Enclosed systems offer superior control over culture conditions but are more expensive than open systems. Algae can be cultivated on non-arable land using brackish or salt water and have higher theoretical productivity in biomass per unit time than traditional land crops. Genetic engineering of algal genomes provides opportunities to add additional value to their cultivation. The promise of algal biotechnology lies in using photosynthetic microbes to grow in wastewater using solar energy to capture nutrients that would otherwise be discarded and convert them into specific chemicals of interest. Algal cells' organellar compartmentalization provides a platform for producing non-glycosylated recombinant proteins in the chloroplast or glycosylation of proteins in the endoplasmic reticulum (ER) and subsequent secretion. Algal cells may also be favorable eukaryotic environments for metabolic engineering approaches to produce specialty metabolites by expressing vascular plant enzymes. However, several barriers hinder the broad implementation of algal species as host cell systems for molecular engineering. Photosynthetic growth, while advantageous from a sustainability perspective, also requires infrastructure considerations to ensure adequate light penetration and carbon dioxide supply into cultivation vessels, factors that generally yield lower volumetric cell densities than fermentation. Nevertheless