Oysters are farmed worldwide and one of the main problems is infestation by polydorin polychaetes. The native Crassostrea gasar and the exotic Pacific Crassostrea gigas oysters support aquaculture production along the subtropical southern Brazilian coast. Worm infestation rates in the two oyster species were evaluated, hypothesizing that infestation is related to stocking densities and hydrodynamic intensity. The main oyster production areas in Brazil were sampled: Parana state, Medeiros (25° 22′ S, 48° 27′ W), Ponta Oeste da Ilha do Mel (25° 29′ S, 48° 22′ W), and Cabaraquara (25° 49′ S, 48° 34′ W) and the Santa Catarina state, Riberão da Ilha (27° 43′ S, 48° 33′ W). Generalized linear models were performed to analyze the effects of sites characterized by different stocking density, hydrodynamic intensity and mean sea surface temperature (SST), the condition index, and the oyster species (native or exotic). Polydorin infestation was higher (mean of 6.02 polydorins/oyster) under higher oyster stocking densities and intermediate hydrodynamic intensity sites (Riberão da Ilha, in the Santa Catarina state). In Parana State, the two sites with similar stocking densities, Ponto Oeste (7,638 oysters/m²) and Cabaraquara (7,550 oyster/m²) presented a higher polydorin infestation in the site with low hydrodynamic intensity and higher mean SST (5.34 vs. 2.64 polydorins/oyster, respectively). The condition index was not impacted by the polydorin infestation. Native C. gasar showed a higher polydorin infestation than the exotic C. gigas (6.02 vs. 1.36, respectively), indicating a higher vulnerability to worm infestation. These results may lead to a better understanding of the infestation patterns of locally grown oysters and to the implementation of better farming management.