The mitochondrial DNA has been used widely in molecular baraminology studies. Besides the mitochondrion, the chloroplasts of plants harbor an entire organelle genome, which can also be used to identify putative groups, which can be compared to those identified in studies based on mitochondrial DNA, nuclear DNA, and morphological characters. The ten-fold size of the chloroplast genome allows a much larger sequence space to be analyzed, but it also brings its own set of analytical challenges to the table. In this study, the chloroplast genomes of 163 species from the plant order Liliales were examined, with the genus Stemona (order Pandanales) as an outgroup. A multiple alignment was created, and a sequence similarity matrix was derived from it, which was then clustered into several putative holobaramins. Of these, six groups had more than five members. These putative baramins are: Tulipa+Amana, Disporum, Fritillaria+Lilium+Nomocharis+Notholirion, Daiswa+Paris+Trillium, Smilax, and Veratrum . Compared to the results of a previous morphological analysis, there are some discordances. The previous analysis separates Trillium from Daiswa and Paris, and unites Alstroemeria with Disporum. Ultimately, genetics should decide baraminic classification, albeit the chloroplast genome still makes up only a small fragment of the entire plant genome. Following this study, it is hoped that chloroplast genome analysis may enrich the toolkit of molecular baraminology.