Five new species are described in this study: Achnanthidium jiuzhaienis sp. nov., Achnanthidium epilithica sp. nov., Achnanthidium limosua sp. nov., Achnanthidium subtilissimum sp. nov., and Kolbesia sichuanenis sp. nov. Classification was based on light microscopy (LM) and scanning electron microscopy (SEM). A. jiuzhaienis sp. nov. belongs to the “A. pyrenaicum complex” of the genus Achnanthidium, this classification was based on certain characteristics, such as the possession of transpically-elongated areolae and deflected external distal raphe fissures. A. epilithica sp. nov., A. limosua sp. nov., and A. subtilissimum sp. nov. belong to the “A. minutissimum complex” of the genus Achnanthidium, this classification was based on certain characteristics, such as the possession of straight external distal raphe fissures and round or elliptical areolae. Kolbesia sichuanenis sp. nov. was found to belongs to the Kolbesia genus, based on its elongated areolae and striae comprised of one macroareola. All five species were sufficiently different from other similar species to be considered unique separate species based on their valve outline, shape of the axial and center areas, and density of striae of each taxon. These new species derived from the epilithic and epiphytic collections of four alkaline lakes in Jiuzhai Valley, Sichuan Province, Southwest China.