Marine phanerogams are ecosystem engineers, as their presence induces major environmental changes that impact on the benthic fauna. Consequently, modifications to the structure of benthic communities would be expected to be associated with seagrass decline. Since 2005, Zostera noltii seagrass beds in Arcachon Bay (France), the largest in Europe, have undergone a severe decline. Twelve stations distributed throughout the lagoon were sampled in 2002, and all were found to be densely planted at that time. Subsequently, the same stations were revisited in 2010 and seagrass cover had drastically decreased by that time. Based on benthic macrofauna, multidimensional scaling (MDS) analysis identified four groups. Years were separated. In 2002, two groups were distinct in relation to the water body, since in 2010 separation between the two other groups was related to seagrass occurrence. When looking at community structure and dominant species there were moderate differences within and between years, independent of seagrass decline. Seagrass loss did not drastically modify the species composition as they were preserved in the remaining seagrass patches. However, there was a drop in macrofauna abundance in unvegetated muddy compared with abundance in the remaining seagrass areas. Epifauna was particularly affected by seagrass decline. Among biotic indicators based on macrofauna, multivariate indicator MISS (Macrobenthic Index in Sheltered Systems) was in agreement with the similarity of macrofauna structure among groups, while other tested indicators performed badly in relation to seagrass occurrence. However, no index detected seagrass loss, highlighting the necessity of maintaining a separate survey on seagrass cover.< Réduire