Aquaculture development suitable location is not formulated from one criterion but from multiple criteria. A list of criteria was selected by reviewing the literature and consultation with aquaculture experts and then classified into five categories namely; water, soil, support, infrastructure and risk factor. Using these criteria a Mahalanobis Taguchi System (MTS) based tool was developed to facilitate the selection of prime set of criteria, which is a subset of the original criteria for suitable aquaculture site identification. Mahalanobis Distance (MD) was used for constructing a measurement scale for the aquaculture system. The principles of Taguchi method was used for screening the important criteria in the system. The information required to make an assessment was entered into the computer program. The computer program then processes the information and produces the prime set of criteria for each category. The software program is a valuable tool for the identification of prime set of criteria within each category. One can use these prime set of criteria within each category instead of all criteria for the identification of optimal location in shrimp aquaculture.