Marine environment remains to this day, the most diversified ecosystem on Earth and simultaneously the least studied. Marine organisms cope with the several challenges that marine life represents, like low temperature and light availability and high pressures, by synthesizing a number of molecules that constitute a potential source of bioactive compounds to be used in human therapeutics. In fact, several biomedical products have been obtained from marine organisms and are currently under clinical trials to treat various pathological conditions, such as cancer, inflammation and allergy.

In this chapter we will focus on the recent trends in the area of metabolomics that led to the characterization of cytotoxic molecules (peptides, macrolides, alkaloids, terpenes, among others) from marine organisms, with special emphasis on invertebrates. The involved cellular targets and mechanisms of cell death will be also overviewed.

In addition, the main analytical techniques used in metabolomics, such as liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance, will be discussed.