We analyzed 25 chloroplast simple sequence repeat (cpSSR) loci in 82 accessions, 59 of cultivated radish and 23 of three wild Raphanus species and identified 7 polymorphic loci and 20 haplotypes. The distribution of haplotypes in different species and different geographical areas was assessed. Minimum-spanning network (MSN) was used to identify phylogenetic relationships in cultivated and wild radish. The MSN provides evidence for at least three independent domestication events, including black Spanish radish and two distinct groups of cpSSR haplotypes. One of these two haplotype groups is restricted geographically to Asia. This led Asian cultivated radish haplotypes to higher cpSSR diversity than Mediterranean cultivated radish or wild radish. These data are consistent with the diversity and distribution of agronomic traits in cultivated radish. At the same time, this implies that Asian cultivated radish is not originated from the diffused descendants of European cultivated radish, probably originated from a wild species that is distinct from the wild ancestor of European cultivated radish. Unfortunately we do not know the wild ancestor of Asian cultivated radish.