With over 400,000 metabolites estimated in plant species, metabolomics is being considered as a promising tool that revealed its efficiency to study the complete set of small naturally present or stresses elicited metabolites. The study led to a comprehensive analysis of metabolites and metabolic pathways in plant tissues. The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterize biochemical interactions of organisms across different spatial and temporal scales. This experimental high-throughput analysis of molecular networks is considered a central approach to characterize the adaptation of plant metabolism to the change in the environment in particular rising temperatures and carbon dioxide enrichment of the atmosphere.