The aim of this work was to analyse genetically natural beds and cultures of the most commercially important mollusc of Santa Catarina (South Brazil), the brown mussel Perna perna. Two sites were chosen for sampling from natural beds and for settling experimental lines with seeds obtained from each local farm. Experimental lines were maintained during four months for evaluating the growth of mussels from different cultures. DNA was extracted by Chelex-Proteinasek method from adductor muscle and amplified by the Polymerase Chain Reaction (PCR) using PMS1 microsatellite primers. Denatured 6% polyacrylamide gel and silver staining were used for separation and visualisation of PCR products, respectively. The nuclear locus obtained showed no significant differences in allele frequencies between natural stocks. Cultured mussels in Penha did not differ genetically from natural beds, but Canto Grande culture was significantly different from the local stock. Mean sizes reached in experimental lines and also from individuals collected in natural stocks were found to be higher in Canto Grande than in Penha. Canto Grande samples showed departure from Hardy-Weinberg equilibrium at the studied locus, due to heterozygote deficiency. The genetic distinction of Canto Grande cultured mussels suggests that seeds from other localities may have been used occasionally by fishermen to set lines for culture.