Natural Guanidines from marine invertebrates represent a group of bioactive secondary metabolites that revealed prominent pharmacological activities such as antimicrobial, antiproliferative, analgesic, and anti-coagulant properties. Acyclovir (Zovirax(®)), the first guanidine-derived pharmaceutical for the treatment of herpes infections since late 1970s, was synthesized based on a marine arabinosyl nucleoside, spongosine. Recently, ziconotide (Prialt(®)), a synthetic form of the marine-derived peptide (ω-conotoxin MVIIA) comprising a guanidine moiety, has been approved for the treatment of chronic pain. This review surveys over 130 compounds of guanidine-containing secondary metabolites from marine invertebrates with emphasis on their pharmacological significance and structure-activity relationships.