Capparis with about 142 taxa is the largest genus in the angiosperm family Capparaceae, and is of high medicinal and economic importance. Several taxa such as C. cartilaginea, C. cleghornii, C. incanescens, C. moonii, C. roxburghii, C. sepiaria, C. spinosa and C. spinosa subsp. himalayensis are difficult to distinguish from each other based on morphology, and they all have partly overlapping geographic distributions. This study assesses the potential of four plastidial loci (rbcL, matK, trnL-trnF, and psbA-trnH) to resolve three species complexes in Capparis. Successful amplification and sequencing, as well as statistical analyses, revealed matK, trnL-trnF, and their combination to be the most effective DNA markers. With these markers we were able to distinguish different Capparis taxa collected from their natural habitats and from the crude drug market. The species rank of C. himalayensis was reinstated based on morphology and molecular data. The phylogenetic relationships of the poorly known C. danielii and C. incanescens with C. sepiaria were clarified.