Antarctic bottoms harbor stable, benthic communities, subjected to low temperatures. Environmental stability may promote the asexual (clonal) reproduction of sponges to maintain adapted genotypes to those particular conditions. Stylocordyla chupachups forms patchy populations across the Antarctic continental shelf. Individuals are mostly similar in size without distinct cohorts, which indicates fast growth of the new recruits. Settlement of incubated (clonal?) functional sponges may accelerate sponge growth and success at early colonization phases. To analyze the weight of clonal reproduction in the species, a genetic study was performed on three close populations using eight polymorphic microsatellite loci that were designed from massive sequencing. The three study populations showed a relatively low genetic diversity and low loci polymorphism (from 2 to 6 alleles). The estimators of genetic structure, the Analysis of the Molecular Variance (AMOVA), and the presence of private alleles indicated low but significant structure between the populations. A relatively high rate of asexual reproduction (ca. 25% of the individuals) was detected. The program MLGsim found five identical multilocus genotypes (MLGs) with an asexual origin. An excess of heterozygotes (in five out of the eight loci genotyped) was found, which suggests a positive selection mechanism for heterozygotes. The relatively high rates of asexual reproduction may be the result of adaptation to the environmental stability, while heterozygote selection would help maintain some genetic diversity in the populations. S. chupachups has been reported to be one of the first sponge species recolonizing bare areas resulting from iceberg scouring, which indicates a high species fitness and adaptation to Antarctic bottoms. Two out of the three study populations showed bottleneck, which may indicate a recent founder effect and supports the pioneer nature of this species.