Marine algae produce a wide range of naturally occurring compounds containing halogen atoms, which play important ecological and biotechnological roles. Algae, particularly marine and macroalgae, are abundant producers of halogenated compounds such as terpenes, phenols, indoles, and acetogenins. These metabolites are primarily produced as part of an organism’s defense mechanisms against herbivores, fouling organisms, and microbial pathogens. Enzymatic halogenation processes involving haloperoxidases, particularly vanadium-dependent haloperoxidases (VHPOs), enable the integration of halogen atoms like iodine chlorine and bromine into organic molecules that are responsible for the structural diversity of halogenated metabolites. This chapter gives a thorough overview of the diversity, biosynthesis, ecological significance, and potential application of halogenated metabolites present in algae. It focuses on the key differences in metabolite profiles among red, green, and brown algae and on impacting factors such as environmental stress, habitat, and species-specific traits that influence their production. Furthermore, it investigates recent advances in analytical techniques to detect and characterize these compounds. Additionally, the pharmaceutical and industrial importance of algal halogenated metabolites with strong antibacterial, antiviral, antifungal, cytotoxic, anti-inflammatory, and antifouling properties is also summarized. However, the sustainable extraction and biotechnological exploitation of these compounds present a significant challenge due to their yield variability, isolation complexity, and ecological constraints which need to be addressed. The development of halogenated-based eco-friendly antifouling and antimicrobial technologies offers a sustainable alternative to synthetic agents protecting nature.