Due to anthropogenic disturbances, the common sponge Petrosia ficiformis has suffered from severe disease outbreaks coincidental with episodic raises in seawater temperature. Here, we report on the optimization of 10 microsatellites that can be used to estimate population connectivity and structure. This information will be critical for further conservation efforts across P. ficiformis’ Atlanto-Mediterranean distribution. Microsatellites were isolated by genomic pyrosequencing and tested in 2 populations from the Mediterranean and Eastern Atlantic, each with 27 and 16 individuals, respectively. The allele number per locus ranged from 4 to 12, observed heterozygosity from 0.399 to 0.686, and expected heterozygosity from 0.421 to 0.715. No linkage disequilibrium between pairs of loci was detected.