Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone contributing to the folding, maintenance of structural integrity and proper regulation of a subset of cytosolic proteins. HSP90 is identified in some crustaceans, however, few studies on the transcript of HSP90 gene in Chinese shrimp Fenneropenaeus chinensis in response to environmental pH and ammonia-N stresses have been reported. In the pH stress experiment, F. chinesis were exposed to marine water with the pH value of 7.0, 9.0 for 148h. During the ammonia-N stress experiment, F. chinensis were exposed to marine water with different concentration of ammonin-N for 96h. The gene expression profiling of HSP90 in different tissues (gill, hepatopancreas, muscle and haemocytes) after pH and ammonia-N stresses were analyzed by quantitative RT-PCR. The HSP90 gene expression in gill, muscle and haemocytes of Chinese shrimp increased when exposed to pH 7.0 and pH 9.0, but the time of the highest gene expression level is different. Obvious different expression of HSP90 gene in hepatopancreas exposed to pH 7.0 and pH 9.0 stress was observed. HSP90 transcripts increased to its highest level post-stress at 3h and then decreased in the pH 7.0 treatment, while in the pH 9.0 treatment the HSP90 gene expression was always higher than that in the control, which indicated the hepatopancreas of Chinese shrimp was the responsive organ to the high pH stress. When the concentration of ammonia-N in marine water was 6 mg/L, the gene HSP90 expression in gill and muscle reached its highest level about 5.46-fold and 1.55-fold respectively post-stress at 24h. HSP90 expression in hepatopancreas and heamocytes in all treatments increased to the maximum value in the range of 1.33~2.08 times and 2.20~5.45 times post-stress at 6h and 48h respectively. The results indicated that the hepatopancreas of Chinese shrimp is more sensitive to ammonia-N stress than other tissues, in which HSP90 expression was up regulated drastically at 6h. It is also illustrated that gill needs higher expression of HSP90 gene than other tissues for cell protection based on the results of the large fluctuation range of HSP90 gene expression in gill. When the concentration of ammonia-N was continuously higher than 2~6 mg/L, the HSP90 expression in all tested tissues was significantly decreased.