Phthalate esters (PAEs), which are widely used in industrial chemicals that serve as important additives to impart flexibility to polyvinyl chloride resins and have become widely diffused in the environment, are considered to be endocrine disrupting chemicals (EDCs). In order to assess the toxicity of PAE to aquatic crustacean, after shrimps (Neocaridina denticulate) were short-term exposed to a sublethal concentration (50 mg/L) of dipropyl phthalate (DPrP), the differential expression genes were isolated and identified using suppression subtractive hybridization (SSH) on the samples prepared from the whole individual. There were 71 unique expressed sequence tags (ESTs) which were identified by homology with data-based sequences, including 23 ESTs corresponded to known genes and 48 ESTs with unknown function. The known genes could be divided into nine classes on the basis of physiological function: genes related to ribosomal, metabolism, immune and structural molecules, concerning the translation-related molecules, involved respiration and signaling, and responding to signaling and vision. By comparing the level of gene transcription in DPrP-treated group vs. non-treated group using semi-quantitative RT-PCR, we found that six of twelve selected genes were significantly up-regulated following exposure to DPrP at high concentration (50 mg/L), including two immune-related genes, one metabolism-related gene and 3 unknown genes. There were eight genes which are significantly responding to DPrP treatment at 1.0 mg/L, including five up-regulated genes (four known genes and one unknown gene) and three down-regulated unknown genes. After exposure to 0.5 mg/L of DPrP, only four genes (three known genes and one unknown gene) were affected and their mRNA levels increased significantly. These results suggest that N. denticulate may be harmed via the change of the globally physiological function following exposure in non-lethal PAE-polluted aquatic environment; in addition, the ESTs derived from N. denticulate can be used for studying the ecotoxicological effect of other pollutants in the aquatic environment.