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Understanding the evolution of sexual vs asexual reproduction and their consequences in population genetics is a central tenet of evolutionary biology. Nevertheless, until now, it has proved unachievable to assess partially clonal reproduction when the rate of clonality is less than 95%, especially without the use of genome-wide data or temporal samples. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. The results of these investigations have been interpreted by comparison with the sexually reproducing congeneric species Laminaria digitata. Genome-wide variation was assessed by dd-RAD sequencing using 4077 SNPs in L. rodriguezii and 7364 SNPs in L. digitata. As predicted for partially clonal populations, the distribution of FIS within populations of L. rodriguezii was centered in negative values, with heterozygote excess at most loci along the genomes. This finding is the opposite of what we reported within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, two distinct distribution patterns of FIS were reported among populations of L. rodriguezii, consistent with the results predicted by the theoretical model for different levels of clonality. These findings highlight that the investment in clonal growth could differ among populations of L. rodriguezii, confirming that the full distribution of FIS is a promising feature to take into account for the study of asexuality in natural populations. We discuss the implications of these results for the conservation of the rare deep water kelp L. rodriguezii.