Microphyll morphology of 16 Taiwanese species of Selagienlla was observed under light microscopy and scanning electron microscopy. Features studied include microphyll arrangement, epidermal cell morphology, stomal distribution, shape arrangement and distribution silica body on microphyll surface. Microphyll are dimorphic and 4-ranked arrangement, with ventral microphylls larger than the dorsal microphylls. The epidermal cells at dorsal side of dorsal microphylls and at ventral side of ventral microphylls are similar, which are tetragonal or oblong in shape and sinuolate or sinuate in anticlinal cell walls. The epidermis at ventral side of dorsal microphylls and dorsal side of ventral microphylls are similar, which are sub-square or rectangular in shape and straight or sinuolate in anticlinal walls. Stomata are mainly distributed on dorsal side of dorsal microphylls and ventral side of ventral microphylls. Four distribution patterns of are found on microphyll silica body, which are microphyll margin, midrib, homogeneity and nil patterns. Four types of arrangement of silica body on epidermal cells were recognized, namely single row, multi-row, mixed and globulate types. In Taiwan, the characters appeared in epidermal cell morphology and stomal distribution of microphyll are useful for species identification in Selaginella, while those of distribution at patterns and arrangement types of silica bodies on epidermal cells are valuable for the species identification under subgenus.