| Summary: | Ria Formosa Lagoon is the most important region for bivalves production in the South Portuguese coast. This study evaluates the microbiological contamination of molluscs <i>Ruditapes decussatus</i> originating from two bivalves production areas of Ria Formosa (a more populated area, Faro–Marchil, and a less populated area, Cacela–Vila Real de Santo António) that were analysed monthly during 1 year. The levels of <i>Escherichia coli</i> and <i>Vibrio</i> spp. were followed and related with temperature profiles. The highest levels of <i>E. coli</i> were found in bivalves collected from Marchil during periods of higher temperatures (summer), mainly due to the population increase during the summer in that area. Although the shellfish harvesting production area classification does not lead to a change in the current classification (Class B). In Cacela higher levels of <i>E. coli</i> were observed especially during the winter, probably due to diffuse sources of faecal discharges. For both areas, the highest levels of <i>Vibrio</i> spp. were found in February and March 2013, these months correspond to a higher level of bacterioplankton in Ria Formosa. Lower levels of <i>Vibrios</i> spp. were found in October 2013 in both bivalve production areas. The analysis of this information can be particularly useful in the development of sanitary surveys and evaluate the human health risks associated with bivalves consumption, thence improving the quality of marketed bivalves, result in adding value to the final product.
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