Xenobiotic phthalate esters (PAEs) are considered endocrine disrupting chemicals and are known to cause immunotoxicity, having been linked with the susceptibility of shrimp to pathogens; however, the effect on other physiological functions has not been explored. This study sought to understand the genetic responses of Neocaridina denticulate, a common freshwater shrimp, to three different PAEs, i.e., diethyl phthalate (DEP), dipropyl phthalate (DPrP), and diphenyl phthalate (DPP). The differential expression of 10 functional known expressed sequence tags derived from N. denticulate were analyzed by semi-quantitative RT-PCR after 24 h of exposure to non-lethal concentrations (0, 0.1, 1.0, and 10 mg/L) of PAEs in pond water. Compared with the control group, nine genes were differentially expressed in the DEP-treated groups, seven genes were differentially expressed in the DPrPtreated groups, and five genes were differentially expressed in the DPP-treated groups. These PAE-affected genes primarily belonged to three functional classes: defense-related genes (qm: QM protein hc: hemocyanin), metabolism-related genes (cathepsin-L like cysteine protease, catl; glutamate dehydrogenase, gdh; and inosine monophosphate dehydrogenase 1, impdh-1) and stress-related genes (hsp70: 70 kDa-heat shock protein; gst: glutathione S-transferase, and tps: trehalose-6-phosphate synthase). Among these, the stress-related genes were significantly up-regulated by DEP, DPrP, and DPP. These effects of PAEs on the expression of genes required for multiple physiological functions suggest that even with non-lethal concentrations of PAEs, a polluted aquatic environment may still present a potential risk to N. denticulate.