For millennia, nature was the only source of medicine for mankind. Even today natural products represent a large proportion of the drugs in use. In some areas, like cancer or infectious diseases, about 50 % of the compounds used are of natural origin. Cyanobacteria, also known as blue green algae are prokaryotic photoautotrophs. They have been on earth for ~3.5 billion years and were able to adapt to almost every conceivable environment. They have evolved to produce a large diversity of secondary metabolites including alkaloids, terpenes, polyketides and peptides. These compounds display a large array of biological activities and are therefore an interesting source for new drugs or biological tools. However they can also represent a threat to humans because of their potent toxic activities. In this thesis we report the isolation, characterization and the biological evaluation of different cyanobacterial secondary metabolites. The first compounds are the heterocyclic ribosomal peptides aerucyclamides A-D isolated from Microcystis aeruguinosa PCC 7806. Their structure was established by NMR spectroscopy and chemical transformation and degradation. We also proposed a structure revision for the microcyclamide 7806A isolated from the same strain. Antiplasmodial evaluation established submicromolar IC50 values for aerucyclamide B against Plasmodium falciparum; low micromolar values for aerucyclamide C were found against Trypanosoma brucei rhodesiense. The compounds were selective for the parasites over a cell line of L6 rat myoblasts and are thus being considered for further study as antimalarial agents. The ecological role of these compounds was also investigated, aerucyclamides A-C were found to be toxic to the freshwater crustacean Thamnocephalus platyurus, exhibiting LC50 values in the range of 30 µM. The second compound, cyanopeptolin 1020 is an aminohydroxypiperidone (Ahp)-containing depsipeptide, which was isolated from Microcystis aeruguinosa UV-006. Its structure was established by NMR and chemical degradation. This compound is a very potent picomolar trypsin inhibitior (IC50 = 670 pM) and also an inhibitor of human kallikrein (4.5 nM) and factor XIa (3.9 nM). Cyanopeptolin 1020 was found to be toxic against the freshwater crustacean Thamnocephalus platyrus (LC50 = 8.8 µM), which is in the same range as some of the well-known microcystins. These data support the hypothesis that cyanopeptolins can be considered as a second class of toxins in Microcystis and may suggest a re-evaluation of drinking water guidelines solely focussing on microcystins at present. In the third part we describe the new microcystin variants [D-Asp3,(E)-Dhb7]-MC-HtyY, [D-Asp3,(E)-Dhb7]-MC-HtyHty isolated from from Planktothrix rubescens strain No80 and MC-RY, [MeAsp3]-MC-RY and [NMeSer7]-MC-YR isolated from a fresh water lake in Uganda. NMR spectroscopy or MS/MS experiments were used to characterize the structure of these potent protein phosphatase inhibitors. The next chapter describes the biosynthesis of nostocarboline, a chlorinated and N-methylated carbolinium alkaloid produced by Nostoc 78-12A. This compound displays potent and selective inhibition of photoautotrophic organisms. New derivatives of nostocarboline incorporating Br, F or methyl substituents have been obtained through precursor-directed biosynthesis. The mode of action of nostocarboline was investigated using chlorophyll-a fluorescence imaging of and it was demonstrated that a decrease in photosynthesis precedes cell death, thus establishing the phytotoxic properties of this alkaloid. In chapters 6 and 7 we describe the evaluation of 27 crude cyanobacterial extracts for anticancer and antiplasmodial activities respectively. For anticancer activity we used the Telospot method to find inhibitors of telomerase, an attractive target for new chemotherapeutic agents. All the extracts displayed telomerase inhibitor activity. By bioassay guided fractionation we were able to identify four sulfoquinovosyl diacylglycerols from Microcystis aeruguinosa PCC 7806 that inhibit telomerase in the micromolar range (IC50 16 µM). For antiplasmodial activity, extracts of Scytonema cf. crustaceum EAWAG 179a, Tolypothrix distorata var. symplocoides EAWAG 224a, Phormidium foveolarum EAWAG 132, Scytonema sp. CCALA 177 and Anabaena flos-aquae EAWAG 116 displayed promising activity against Plasmodium falciparum. In the last chapter we used the cyanobacterium Lyngbya sp. as a model organism for the evaluation of modified surfaces for inhibition of aquatic biofouling. We demonstrated that a PLL-g-(DHPAA; PEG) copolymer layer on a titanium oxide-coated microscopy glass slide successfully prevent attachment of this aquatic phototroph in culture for up to 100 days.