Abstract: One of the challenges of contemporary bio-informatics is how to utilize the huge volume of data and information from high throughput metabolomics and metabonomics studies for reconstructing biochemical network, predicting cell phenotype, optimizing bio-process and evaluating drug safety with novel methods. This paper briefly reviews major methods including supervised as well as unsupervised methods and highlights key issues of bio-informatics analysis within metabolomics and metabolomics research such as extracting and pre-processing data, establishing data standards and integrating with relevant research fields such as genomics, transcriptomics and proteomics. Several important applications in plant, microorganism and mammalian systems are also included and the paper ends up with a prospect of the new ‘omics’.