Evolution of heavy metal tolerance has been described for Orchesella cincta (Collembola) populations originating from metal contaminated mining sites. Genomics tools were applied to reveal if metal tolerance depends strongly on heritable variation in gene. Heritable metal tolerance in O. cincta is correlated with increase of metal excretion efficiency. Tolerant populations demonstrate heritable over-expression of the single copy metallothionein (mt). Population genetic data on natural mt promoter (pmt) alleles indicate an increase of high expression pmt alleles in metal contaminated area’s. Obviously, mt plays a major role in cadmium detoxification. However, an additional number of gene products may be involved in natural selection of metal tolerant phenotypes. Therefore, suppression subtractive hybridization (SSH) was used to isolate differentially expressed genes responding to cadmium. Approximately 2000 SSH clones were spotted on an array and different combinations of hybridisations were performed to study the effect of Cd treatment on gene expression within populations and among populations. Dramatic population specific changes in transcription regulation were observed when a lab culture was compared to a tolerant population: about 32 cDNAs showed Cd induced upregulation of more than 100 fold in lab culture, while a maximum of only eight fold upregulation was observed in Cd-exposed animals from the tolerant population. Real-time RT-PCR on biological replicates confirmed population specific responses of genes involved in cell signalling, transport and programmed cell death. Furthermore, the array data suggest that reference animals, when exposed to cadmium, show a typical transcriptional signature associated with stress, while the tolerant animals maintain normal expression for most of their genes. This may be related to a constitutive or induced detoxification mechanism of cadmium, involving metallothionein and other proteins that prevent toxic free ion concentrations in the cell, despite high exposure.The ecological significance of gene regulation in adaptation to heavy metals is discussed.