This study aims to build up the HSI model to estimate habitat suitability correctly for 7 kinds of benthic animals on a tidal flat in the Yoshino River. We used two or three kinds of physical quantity of median particle diameter, mud content and bed elevation as an environmental influence factor of the object benthos and built up 4 kinds of the HSI model. We selected the most accurate model among 4 models in the reproduction precision of the activity population every animal. The integrated prediction accuracy of the selected HSI models for 7 kinds of benthos is high with 86.5% from 71.5%. Furthermore, we utilized these HSI models, and the habitation prediction map of the benthos was created.