The purpose of this study was to determine the distribution and size of natural stocks of the mussels Mytella guyanensis (Lamarck, 1819) and M. falcata (d’Orbigny, 1846) in the Cananéia–Iguape–Ilha Comprida lagoon estuarine system. Samples of mussels and related information were collected in four areas distributed along Cubatão Sea (I), Trapandé Bay (II), Ararapira Channel (III) and Cananéia Sea (IV) from June 2004 to June 2005. Each area was subdivided in plots that represented the mussels natural banks. The total area occupied by the mussels was estimated. From each one of the 48 delimited plots, 120 samples were collected along 2 transects, summing up 5.760 samples. The animals were counted, measured for length and weight. It was impossible to estimate the stock of M. falcata, due the very low number of individuals. The data presented are from M. guyanensis. The bivalves’ density (nº/m²) ranged from 0.64 to 188.35, showing a heterogeneous distribution among plots. The total area occupied by the bivalves was 438.824 m², with an estimated population of 18.646.453 mussels. Within this population 44.5 % were of commercial size (> 40 mm). The maximum length observed was 72 mm. The most appropriate sites for mussel extraction are located in Cubatão Sea (I) and Cananéia Sea (IV) as these had higher biomass and greater numbers of individuals of commercial size. The results of this research shall contribute to a rational extraction policy.