The objective of this study was to evaluate the microbiological quality of oysters and mussels grown in Cananéia, Brazil, by analysing mesophiles, psychrothophic bacteria, moulds and yeasts, Staphylococcus aureus, and Salmonella spp., and to compare the efficiency of Compact Dry EC method and the conventional method for counting of total coliforms and Escherichia coli. The microbial analysis showed that the mean values of mesophilic counts were 3.14±0.81 log CFU g⁻¹ for oysters and 3.92±0.90 for mussels; the mean values of psychrophilic counts were 2.78±0.75 log CFU g⁻¹ for oysters and 3.22±0.75 log CFU g⁻¹ for mussels; the mean values of mould and yeast counts were 3.70±0.58 log CFU g⁻¹ for oysters and 3.33±0.81 log CFU g⁻¹ for mussels. Salmonella spp. did not present positive results, and the maximal count of Staphylococcus aureus was 1.7 log CFU g⁻¹, therefore, within the limits established in the legislation. The correlation coefficients between the Compact Dry EC method and conventional method were >0.87 for total coliform and E. coli counts for both types of shellfish. The data in this study show that the Compact Dry EC method is an acceptable alternative to conventional methods for enumeration of total coliforms and E. coli in shellfish.