In the present study, the diversity and the stability of the prokaryotic microbiota associated with French Polynesian specimens of the sponge Dactylospongia metachromia are addressed for the first time. Metabarcoding analyses of the holobiont were carried out to study the biogeographical distribution of symbiotic archaeal and bacterial communities within individuals coming from distinct Polynesian archipelagos. We provide a comparison with other locations where the sponge also occurs, like the Indian Ocean or the Red Sea. Investigations of the sponge holobiont were re-conducted on a temporal scale during a farming experiment targeting excised fragments of wild sponge individuals.