Sedum aizoon and S. kamtschaticum have been widely used as useful herbal medical plants, but the relatives have a taxonomic controversy due to their ambiguous morphological boundaries. Thus, at the genetic level, to clarify the taxonomic relationship between the two, we identified the chloroplast DNA haplotypes of 128 individuals from 6 populations in the Korean peninsula. Analyses were based on sequence data from the trnLUAA-trnFGAA, psaI-accD, petN-psbM, and rpl32-trnLUAG regions. The S. aizoon has a total of two haplotypes, while the S. kamtschaticum has a total of five haplotypes. At the species level, S. kamtschaticum harbored relatively higher genetic variation. TCS analysis largely revealed two lineages formed according to each species. However, S. kamtschaticum''s haplotype K1 of the Mt. Jiri population was included in S. aizoon lineage. The haplotype K1 was discussed in two aspects: morphological and genetic criteria in the statistical parsimony network. In this regard, we conclude that S. aizoon specialized for the local environment (Mt. Jiri) was convergent with the morphology of the S. kamtschaticum by chance.