Knowledge of Neogene fish diversity in Taiwan is extremely limited. In this paper, we present a collection of 1716 fish otoliths recovered from the late Miocene Tapu Formation. The abundance and density of otoliths vary across the sites. Although the preservation of samples is considerably limited, our sample coverage is sufficient and reveals the presence of at least 34 otolith-based taxa belonging to 13 families. Four new species are introduced: Larimichthys koae sp. nov., Nibea chaoi sp. nov., Taosciaena jiangi sp. nov., and T. hui sp. nov. Among the earliest fossil records, this collection features a remarkable abundance of Larimichthys spp. The assemblage is dominated by otoliths of Sciaenidae, Gobiidae and Soleidae, and it is indicative of a coastal shallow-water palaeoenvironment with muddy to sandy bottoms, perhaps adjacent to a river mouth. We hypothesise that the differences in the taxonomic composition between the fossil assemblage and modern fauna are mainly chronological and evolutionary, and only a moderate turnover of certain lineages has occurred since the Miocene. Our study provides a unique 'window' to a rarely visited fossil fish community that exclusively documented by fossil otolith data, and reveals a past coastal fish diversity that otherwise could not be recognised.