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Cenchrus ciliaris L. is a C-4 perennial grass of arid lands which is under the focus of different ecological issues such as response to desertification, quality of forage grass and impacts of invasions. Here, molecular and morphological analyses of the genetic diversity of several Tunisian provenances of C. ciliaris were performed to better understand the phenotypic polymorphism of this agamospermous and polyploid grass. Ten phenotypic traits associated with productivity were measured in a common garden environment. Amplified Fragment Length Polymorphism (AFLP) markers were developed to investigate the structure of genetic diversity among and within provenances and between the three ploidy levels. Heritable phenotypic traits showed considerable differences within provenances. Surprisingly, AFLP markers revealed the existence of genotypic variations between individuals of the same sibship and a high G/N value (0.55). A neighbour-joining tree based on AFLP markers revealed three major groups; tetraploid, pentaploid and a mix of pentaploid and hexaploids. These groups do not correspond completely to the geographical origin of samples. The results underline the possibility of sexual reproduction, recombination and gene flow within and between populations of C. ciliaris. In respect with the well known dynamic nature of polyploid genomes, these results should have strong consequences for the future management of this grass for both conservation and invasion issues.