Sanicula (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five Sanicula species (S. flavovirens, S. giraldii, S. lamelligera, S. odorata, and S. rubriflora) were sequenced and compared to the previously published S. orthacantha plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci rpl2, matK, psbA, and ycf1 are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup Hydrocotyle (Araliaceae) reveal sectional relationships in Sanicula different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. Sanicula orthacantha and S. chinensis form a clade sister group to S. lamelligera and S. odorata, consecutively. These four species comprise a clade sister group to the clade of S. rubriflora and S. flavovirens, with this entire group sister to S. giraldii. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of Sanicula.