We have used polymorphic chloroplast simple sequence repeats (cpSSRs) to analyse levels of diversity and relationships within the genus Zea. Between two and nine alleles were found at 15 polymorphic loci and combining the data from these loci gave 32 haplotypes in the 37 accessions studied. Genetic differentiation between the two sections within the genus was calculated using the PST statistic which showed that similar to 70% of the total variation was found to exist between the sections. A phylogenetic analysis based on the delta mu(2) distance metric showed a large split between the two sections and suggested multiple origins of modern cultivated maize Zea mays subsp. mays. The agreement of the phylogenetic tree with other molecular, morphological and karyological studies suggests that cpSSRs may have value in phylogenetic studies in plants.