The recurrent lack of Isolation By Distance (IBD) reported at regional scale in seagrass species was recently suggested to stem from stochastic events of large scale dispersal. We explored the usefulness of phylogenetic information contained in microsatellite loci to test for this hypothesis by using the Genetic Distance Spectrum (GDS) on databases containing microsatellites genotypes for 1541 sampling units of Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase of microsatellite and geographic distances that emerges, reveals a coherent pattern of IBD in contrast to the chaotic pattern previously described using allele frequencies, in particular for the long- lived P. oceanica. These results suggest that the lack of IBD, rather than the resulting from rare events of large scale dispersal, reflects at least for some species a stronger influence of mutation over migration at the scale of the distribution range. The global distribution of genetic polymorphism may therefore result predominantly from ancient events of step-by-step (re)colonization followed by local recruitment and clonal growth, rather than contemporary gene flow. The analysis of GDS is appears useful to unravel phylogenetic information borne by microsatellites, under an appropriate mutation model, to unravel the evolutionary forces influencing the dynamics and evolution at distinct temporal and spatial scales. This finding nuances the generalization of the influence of large scale dispersal on the dynamics of seagrasses.