Micro-algae (prokaryotic and eukaryotic) are increasingly used in food production, biotechnology and water treatment. By developing a high throughput screening system for naturally occurring micro-algae strains, we aim to expand the pool of strains available for biotechnology and other applications. We are implementing genomics and analytical tools in our pipeline to obtain detailed information about the metabolic and genetic profiles of the micro-algae strains extracted form environmental samples. This information will be valuable in identifying strains with specific properties or characteristics relevant to industries. We are partnering with cFortySix Solutions to test the proof of principle of the screening system and are focusing on local species from rivers and lakes in Ontario. This collaboration provides unique expertise and resources, which are invaluable in optimizing the screening pipeline and analyzing the results. Our approach has the potential to lead to the discovery of new strains with unique metabolic pathways, which can be exploited for the extraction of valuable compounds or for the removal of toxic compounds from the environment.