In regard to the degradation of water quality since the last decades, appropriate diagnostic tools have been implemented. In France, water agencies in collaboration with Cemagref have developed a diatom index to estimate global water quality. The Biological Diatom Index (BDI, Coste et al. 2009) is routinely used for monitoring applications in European territories and has been standardized (NF T 90-354). Nevertheless, indices currently used for water quality assessment don't take in consideration metal contamination in their conception, despite the high bioaccumulation and impact shown on periphytic diatom communities (da Silva et al., 2009, Cunningham et al., 2005, Feurtet-Mazel et al., 2003). Moreover these methods are time consuming and require important taxonomic knowledge. In this context development of q-PCR approaches are of particular interest. In our study we have developed a new RNA extraction method for diatoms, 8 genes of interest for the diatom Eolimna minima have been selected, sequenced and deposited in the GenBank. The responses of the q-PCR tools developed have been tested after Cd exposure on Eolimna minima. Bioaccumulation and population kinetics were also followed.