Perna perna(Linnaeus, 1758) is the main marine bivalve mussel yielded commercially in Brazil. In spite of this, scientific data is very scarce regarding its productivity in tropical shallow waters. The Condition Index (CI) is used worldwide in mariculture to assess animal health, harvest time, and yield. In this study, the authors used CI results from nine different methods to assess the season effect on the mussel CI and also to evaluate the potential yield of three southern Brazilian bays. The results from nine CI methods were used for the comparison of the seasonality and yield of mussels reared in three marine bays. Sampling was carried out monthly within two 4-month periods, from December 2008 to August 2009. The results show a trend for seasonal effects on the CI results. The winter months showed the highest and the lowest values. Between bays, higher CI values were detected in animals reared at Sepetiba Bay, followed by Guanabara Bay and Ilha Grande Bay. We suggest that the CI (that considers the ratio between bivalve soft tissue wet weight and total length) should be used by fishermen, since this formula was able to detect differences between sites and is more easily applied.