The marine ecosystem is still an untapped reservoir of biologically active compounds, which have considerable potential to supply food ingredients towards development of new functional foods. With the goal of increasing the availability and chemical diversity of functional marine ingredients, much research has been developed using biotechnological tools to discover and produce new compounds. This review summarizes the advances in biotechnological tools for production of functional ingredients, including enzymes, for the food industry. Tools involving biotechnological processes (bioreactors, fermentations, bioprocessing) and those involving genetic research designated as molecular biotechnology are discussed highlighting how they can be used in the controlled manipulation and utilization of marine organisms as sources of food ingredients, as well as discussing the most relevant shortcomings towards applications in new functional foods. ► Marine biotechnological advances review for production of functional ingredients. ► Biotechnology tools using marine organism as sources of food ingredients are included. ► Challenges associated with functional foods containing marine ingredients are pointed. ► Functional ingredients interest increases with role diet plays in consumer’s health.