Deltamethrin is a class II pyrethroid insecticide commonly used in agriculture. It is hazardous to freshwater ecosystems, especially for the cladoceran Daphnia magna (Straus 1820). The results of our previous studies based on acute and chronic ecotoxicity experiments revealed differences in the sensitivity between two different clones. In this work, to investigate deltamethrin toxicity mechanisms in two clones of D. magna, we used a proteomic approach in order to analyze changes in protein expression profiles after 48h of exposure. We detected 1339 spots; then applying statistical criteria (ANOVA p<0.001 and minimum fold change 1.5), only 128 spots were significantly different in the normalized volume. Among the preselected proteins there were 88 up-regulated and 40 down-regulated proteins. Results showed differences in sensitivities after deltamethrin exposure between the clones. Moreover, using the 2-DIGE method, proteomic investigation for deltamethrin exposure proved to be a reliable and powerful approach to investigate effects of deltamethrin as part of research for new metabolic and cellular biomarkers. After identification by mass spectrometry, there were 39 proteins recognized and identified, in which 21 and 18 were up- and down-regulated, respectively, in deltamethrin-exposed clone A compared to three other conditions (controls of each clone and deltamethrin-exposed clone 2). Up- and down-regulated proteins belonged to 12 biological processes (i.e. metabolic processes, apoptosis and stimulus response) and 5 molecular functions (i.e. catalytic activity, binding, structural molecular activity, antioxidant and receptor activities). Identification of these deregulated proteins opens a new way in discovering new molecular targets and putative biomarkers in daphnids exposed to deltamethrin.