Freshwater and terrestrial cyanobacteria resemble the marine forms in producing divergent chemicals such as linear, cyclic and azole containing peptides, alkaloids, cyclophanes, terpenes, lactones, etc. These metabolites have wider biomedical potentials in targeting proteases, cancers, parasites, pathogens and other cyanobacteria and algae (allelopathy). Among the various families of non-marine cyanobacterial peptides reported, many of them are acting as serine protease inhibitors. While the micropeptin family has a preference for chymotrypsin inhibition rather than other serine proteases, the aeruginosin family targets trypsin and thrombin. In addition, cyanobacterial compounds such as scytonemide A, lyngbyazothrins C and D and cylindrocyclophanes were found to inhibit 20S proteosome. Apart from proteases, metabolites blocking the other targets of cancer pathways may exhibit cytotoxic effect. Colon and rectum, breast, lung and prostate are the worst affecting cancers in humans and are deduced to be inhibited by both peptidic and non-peptidic compounds. Moreover, the growth of infections causing parasites such as Plasmodium, Leishmania and Trypanosoma are well controlled by peptides: aerucyclamides A-D, tychonamides and alkaloids: nostocarboline and calothrixins. Likewise, varieties of cyanobacterial compounds tend to inhibit serious infectious disease causing bacterial, fungal and viral agents. Interestingly, portoamides, spiroidesin, nostocyclamide and kasumigamide are the allelopathic peptides determined to suppress the growth of toxic cyanobacteria and nuisance algae. Thus cyanobacterial compounds have a broad bioactive spectrum; the analysis of SAR studies will not only assist to find out the mode of action but also reveal bioactive key components. Thereby, developing the drugs bearing these bioactive skeletons to treat various illnesses is wide open. Copyright © 2012 John Wiley & Sons, Ltd.