Contamination of aquatic systems by metals and polycyclic aromatic hydrocarbons (PAHs) is a prevalent environmental problem. These contaminants are known to impact populations, organismal health, and survival negatively. Most of the organism and ecosystem level changes are a consequence of underlying molecular and subcellular damage. Therefore, molecular bioindicators are likely to be a sensitive tool for environmental assessment. We have demonstrated that both copper and phenanthrenequinone (PHEQ) alter protein expression in Daphnia magna. To investigate altered gene expression in Daphnia magna exposed to copper, PHEQ, and other contaminants, a technique based on the differential display polymerase chain reaction (ddPCR) is being developed for D. magna. This technique promises numerous applications as it permits a survey of the genes being expressed in any given organism. Furthermore, ddPCR allows one to monitor the changes in gene expression that result from any toxicant exposure. This paper reviews the applications of ddPCR and describes our development of ddPCR as a bioindicator of gene expression in D. magna in response to toxicant exposure. This is the first step in the development of a novel gene fingerprinting technique that can be applied to any compound and organism of interest.