The genus Sanicula L. possesses many medically important plants, belonging to the family Apiaceae. It is one of the most taxonomically difficult taxa, largely due to the great variability in habit, foliage, flowers and fruits. Previous studies have mainly focused on the molecular studies of this genus, and the morphological research for this genus was limited, especially in the micromorphological research. In the current study, we newly obtained leaf materials from twenty-two Sanicula members, fruit and pollen materials from twenty Sanicula members and performed comprehensively micromorphological analyses for this complicated genus. The results of the leaf epidermis showed that the upper and lower epidermis were smooth and glabrous, and the cell shape was polygonal or irregular. The patterns of anticlinal wall were shallowly undulating, deeply undulating, subflat or flat. The cuticular membrane ornamentations were diverse, and some species had epidermal appendage. All Sanicula species observed the stomata in the lower epidermis, and only five species (S. rugulosa, S. elongata, S. hacquetioides, S. tienmuensis and S. elata) observed stomata in the upper epidermis, which can easily identify them from other Sanicula members. In addition, we found that the fruits scarcely compressed, and some fruits had their distinctive shape, such as the fruit shape of S. tienmuensis was subglobose, S. subgiraldii was broadly ovate and S. pengshuiensis was ellipsoid. All Sanicula taxa fruits surfaces were covered with prickles, bristles, protuberance, or tubercles, prickles were either long or short, uncinate or straight, rarely scale-like, ribs inconspicuous or slightly prominent, but the prickles/bristles/tubercles were different in shape, sparseness and arrangement. The vittae were distinct in S. rubriflora, S. chinensis, S. caerulescens, S. pengshuiensis, S. pauciflora, S. lamelligera, S. oviformis, S. flavovirens and S. elata, and the remaining taxa were obscure. These findings indicated that the fruits can clearly distinguish these Sanicula members. Furthermore, the micromorphological characteristics of pollen showed that the equatorial view included four shapes: ellipsoid, subrectangular, equatorially constricted and super-rectangular-equatorially constricted; and the polar view possessed four shapes: triangular, triangular-circular, suborbicular and trilobate circular. The germ furrow and the outer wall ornamentation of all Sanicula taxa were quite similar, indicating that the genus was a natural unit. In summary, our study promoted the improvement of a taxonomic system for the genus and also provided additional evidence for future taxonomic study of the genus Sanicula.