Perna perna is the most important cultivated mussel of Santa Catarina, Brazil, sustaining an important economic input for many local families. Natural stocks of P. perna are depleted by the extraction of adults and seeds for consumption and culture. The aim of the present study was to use the microsatellite locus pms-2 to study the variation of the genetic composition and diversity between natural and cultured stocks in samples of 2001 and 2005 from Penha, Santa Catarina. DNA was extracted from adductor muscle by Chelex/proteinase-K and phenol/chloroform protocols. Amplification by polymerase chain reaction was performed using specific primers for analyzing the pms-2 locus. Polymerase chain reaction products were submitted to vertical denatured 6% polyacrylamide gel electrophoresis and horizontal 2% agarose gel electrophoresis, and visualized by silver staining and ethidium bromide, respectively. Allele diversity and heterozygote deficiency were higher for samples of 2005 than for those of 2001. No significant genetic differentiation was found between natural and cultured stocks of 2001 by the c2 test, but G2 (likelihood ratio) detected slight differences (I = 0.949; c2, P = 0.147; G2, P = 0.046), while cultured and natural stocks of 2005 were very different (I = 0.798, P = 0.006). Between the years of 2001 and 2005, a large change in genetic composition was observed (I = 0.582; P < 0.001). Although nothing is known about natural changes in the genetic composition of this species with time, the results suggest a strong impact of human activities on natural stocks of P. perna, which is expected to be related to heavy extraction and farming