In order to examine the usefulness of detoxifying genes as molecular markers in different chemical environments, isolation of cytochrome P450 genes (CYPs) belonging to the CYP4 family was performed in different samples from two subalpine populations of Daphnia pulex. The use of degenerate primers allowed us to isolate seven cDNAs. Four of them were assigned to the CYP4C subfamily, and were closely related to previously isolated crustacean CYP4s while the others were assigned to new CYP4AN and CYP4AP subfamilies. Expression studies, using semiquantitative polymerase chain reaction (PCR) followed by Southern blot hybridization with specific probes revealed differences in CYP4C32 and CYP4AP1 expressions between the two populations, which differ in the polyphenol richness of the vegetation surrounding their aquatic habitat. Further exposure to toxic dietary polyphenols showed different CYP induction patterns. Taken together, these preliminary results suggest a possible involvement of CYP4s in the ecological differentiation of subalpine D. pulex populations related to the polyphenol richness of the environmental vegetation. CYP4s may thus be considered as possible molecular markers in aquatic environmental bioreporting.