In this paper, faunal remains unearthed from six shell midden sites along Yong River are discussed. Within these seven classes, 84 species are identified. Diachronic and synchronic studies of these taxa demonstrate the biodiversity of the Yong River shell midden sites. The four archaeological phases represent the entire process of initial origination, later development, and final disappearance of the shellfish cultural deposits. The types of species, quantity and body size show significant similarities and differences between the sites in each stage.