European stocks of the Manila clam Ruditapes philippinarum are affected by the Brown Ring Disease (BRD), which is caused by Vibrio tapetis. BRD is characterized by an accumulation of a brown organic matrix on the inner face of the shell. Clams that recover from BRD develop a white mineralized layer covering the brown matrix. Stocks of clams that showed resistance to BRD development, as enhanced recovery, have been monitored since 2000. We have examined two selected stocks: a Low Susceptibility (LS) stock and a High Susceptibility stock (HS), over three generations. The LS stock showed less evidence of the BRD symptoms, and more evidence of total shell repair, both in the field and following experimental challenge with V. tapetis, indicating that some clams may be less vulnerable to a V. tapetis attack than others. The inner face of the valves of the LS and HS clams of the two last generations were analysed with scanning electron microscopy. Examination of shells from BRD-affected clams showed that during the repair process, calcium crystals were progressively laid down until the affected zone was entirely covered. By the end of the shell repair process, a final organic layer covered the calcium crystal mounds. This layer seemed essential in the recovery process. The results indicate that the shell repair capability of the clams is the principal mechanism implicated in the development of BRD resistance in the Manila clam stocks. However, this resistance did not increase with generation because the broodstock was maintained at a site where selection pressure was low, due to a low prevalence of V. tapetis.