Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://bioinfo.csie.ncu.edu.tw/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence. The supplementary data is available on the web at http://bioinfo.csie.ncu.edu.tw/ RiboSW/sup.pdf.