Bioremediation is nowadays widely accepted as an effective strategy for the recovery of contaminated soils; however the lack of information about the factors that govern the metabolic functioning of microbial communities in contaminated environments means that, still at present, the bioremediation processes have unpredictable results. The molecular techniques based on DNA studies have allowed the identification of numerous catabolic genes opening new opportunities in the development of bioremediation processes. In this new post-genomic era, emerging metatranscriptomics, metaproteomics and metabolomics are remarkable promises as tools to study the mechanisms involved in the regulation of degradation pathways, which in the future will allow us to develop predictive models of degrading activity of the soil microbial community according to the various biotic and abiotic parameters, establishing specific and clear criteria for the selection and evaluation of bioremediation strategies.