In Europe, shellfish harvesting areas are classified according European Directive EC N°854/2004, using classic faecal indicator levels (Escherichia coli). A better indicator is needed, however, because shellfish may contain other human pathogens. Other indicator organisms have therefore been evaluated and, among these, coliphages meet most of the requirements to serve as indicators and models for enteroviruses. In order to evaluate the capacity of coliphages as indicators, a total of 764 shellfish were sampled in 2004 from 70 shellfish harvesting areas monitored by the Ifremer microbiological surveillance network (REMI, http://www.ifremer.fr/envlit/), and tested for F-specific RNA bacteriophages (FRNAPH). Two species of bivalve mollusc were collected monthly: blue mussels (32%) and Pacific oysters (68%). Results showed the absence or weak presence of bacteriophages in most shellfish growing areas classified A (94% of shellfish were below 1000 PFU (Plaque Forming Units)/100 g). These data are important for evaluating the potential of FRNAPH to discriminate between sources of pollution. Genotyping of FRNAPH may differentiate between human and animal contamination. Our results show that genotyping should be possible in 43% of the studied sites when the total flesh is analysed. As digestive tissues are known to concentrate micro organisms, this percentage could be increased if analysis were performed on them. The FRNAPH method, used with other discrimination markers, could help both states and regions to make investment decisions on how to recover suitable sanitary quality in shellfish rearing areas. For example, contamination observed in clam samples collected in Daoulas estuary (Brittany) was shown to be of mainly animal origin. Similar results were obtained on oysters from Thau lagoon (Mediterranean coast), collected during dry weather.