Ceropegia lodarensis (≡ Huernia lodarensis) is a succulent plant with medicinal uses in Arabian folk medicine. It belongs to Ceropegia sect. Huernia, the most diverse and widespread section of the highly succulent plants informally known as stapeliads. Morphological identification of this species is difficult and often impossible without flowers. This study tested the performance of three DNA barcodes: the nuclear ribosomal internal transcribed spacer (ITS) region, plastid psbA–trnH intergenic region, and noncoding plastid trnL–trnFto identify C. lodarensis at the molecular level using BLASTn searches and tree-based methods, namely maximum likelihood (ML), maximum parsimony (MP) and neighbour joining (NJ). Results showed that the candidate regions have a low species-level resolving ability. However, ITS has the highest identification success rate at the sect. Huernia level, suggesting its potential for plant identification systems of Huernia species at the section level. Additional work is needed to examine the utility of further DNA loci.