This paper describes one new Gomphonema species from Yunnan Province, China, including valve morphology based on light and scanning electron microscopy. The species, Gomphonema bigutianchnensis sp. nov., is similar to many species of the genus in the organization and structure of the areolae, raphe, stigma and apical pore fields. It differs from known species in the shape of the valve and in length/breadth measurements. This species is distinguished by the broadest portion being positioned towards the wedge-shaped and rounded headpole. We compared these species to those of similar shape and morphology, and provide information about its ecology.