Based on the light and scanning electron microscopy observations, we present a detailed description of a new brackish diatom Navicula amoyensis sp. nov. Samples were collected from an intertidal sand flat in the Jiulong River estuary, Southern China. The key diagnostic features of this species include the simple terminal raphe endings, broad terminal area, two rows of perpendicular apical pores, a wide contracted girdle region with pectinate margin and internal proximal raphe endings with a raised siliceous rib and accessory rib. Furthermore, the main taxonomic features of N. amoyensis sp. nov. and the genera Hippodonta and Navicula are also discussed in detail.