The variation of the composition of assemblages and the relative abundance of commercial prawns collected from the coastal waters of Yunlin was studied. The data of shrimp fishery was collected from Jan 1997 to Dec 2008 through the program of Integrated Assessment and Management of Environmental Resources for the Industrial District on the Outer-Bank of Yunlin Islands. The dominant species landed in this area are Parapenaeopsis hardwickii, Metapenaeus ensis, and Penaeus penicillatus. Their peak catch seasons are November to May, March to August, and July to March, respectively. The composition of the assemblages of commercial shrimps belonged to three groups according to the seasons: winter (December to February), spring to summer (March to July), and late summer to autumn (August to November). According to time series analysis, the relative abundance is auto-regressed to that of the previous month and the same month one year age. In addition, Jhuo-Shuei river runoff ware correlated to a significant decrease of the shrimp abundance five months later. Based on this information, we obtained a seasonal and factored ARIMA time series equation of the relative abundance of commercial shrimps.