Fritillaria is a taxonomically complex genus of Liliaceae that contains many important ornamental and medicinal species. In this study, we sequenced the chloroplast genomes of ten Fritillaria species distributed in Central Asia and compared them to previously sequenced Fritillaria cp genomes. Comparison of 36 Fritillaria species’ cp genomes identified as useful potential molecular markers due to their high level of divergence three coding regions and 11 intergenic spacers. Effective single sequence repeats (SSRs) for population genetic studies of Fritillaria were also identified. Phylogenetic analysis showed that two recently described species, F. baisunensis and F. rugillosa belong to subg. Rhinopetalum, and that the membership of F. ussuriensis and F. meleagroides in subg. Fritillaria should be revised. These two species and F. camschatsencese currently assigned to subg. Liliorhiza, should be members of the same taxonomic unit. Subg. Liliorhiza, although a small group, is more complicated that it was previously thought, and apparently comprises species too distant to be in one subgenus. F. maximowischii, currently assigned to subg. Liliorhiza should be treated as a new subgenus.