Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are indeed irreconcilable with clonality. The genetic structure and diversity of clonal plant populations was examined using a combination of new tools to analyze microsatellite data in the marine angiosperm Posidonia oceanica. These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of regular immigration from distant populations seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed that populations follow a "small-world" topology, characterized by a high degree of connectivity among nodes, and a high hierarchical substructure, revealing a structure in sub-families of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intrapopulation genetic structure of the clonal plant investigated; these therefore represent promising alternative analytical tools in evolutionary ecology.