Intra-organismal genetic variation is not automatically detrimental as in cancer or senescence. Modular, asexually propagating species comprise an ecologically important group of animals and plants in which somatic mutations may provide an alternative pathway to evolutionary adaptation. Theory predicts that (i) somatic mutation rates may exceed the meiotic input, (ii) somatic genetic diversity can be partitioned among modules to create phenotypic heterogeneity subject to selection, and (iii) somatic mutations are transferable into the sexual cycle because plants and basal animals do not have an early-sequestered germ line. We have started to test above predictions in a widespread temperate seagrasses species, Zostera marina, characterized by long-lived, clonal lineages that extend over hundreds of meters to kilometres, and where a good genomic resources have recently become available. We employ deep re-sequencing to track and categorize somatic mutations with respect to putative function and genomic location in space and time. These approaches can also be extended to reef-building corals. These results will close a critical gap in our understanding of adaptive evolution in modular-clonal organisms that may inform better strategies for restoration efforts in foundation species threatened under global change.