Eight microsatellite loci were characterized in the colonial ascidian Pycnoclavella sp. from an enriched library of genomic DNA. Most microsatellites were large and compound. Allelic variation was assessed in 30 individuals collected from Cerro Gordo (SW Mediterranean Sea). The number of alleles per locus ranged from one to nine, observed heterozygosity from 0.05 to 0.29 and expected heterozygosity from 0.15 to 0.39. No significant linkage disequilibrium between pairs of loci was detected, but five loci showed significant heterozygote deficiency that may be explained either by inbreeding, population substructure or the presence of null alleles