Mestrado Management and Conservation of Natural Resources - Instituto Superior de Agronomia - UL / Universidade de Évora ; Seagrass beds provide higher biomass, abundance, diversity and productivity of ichthyofaunal communities than non-vegetated substrata. During 2008, the seagrass beds of Zostera noltii located in the lower Mira estuary (SW Portugal) disappeared completely. However, during 2009, slight symptoms of natural recovery were observed, a process which has since evolved intermittently. The main goal of this study was to investigate the temporal and spatial distribution patterns of the composition and structure of the ichthyofaunal communities under two distinct habitat ecological conditions: “before” the collapse, characterized by mature vegetation of the seagrass beds, and “after” recovery, corresponding to natural habitat recovery process of the seagrass beds. The following hypotheses were tested: there would be significant differences of the fish communities between i) the period “before” the habitat loss and “after”, during the natural recovery; and ii) seagrass beds and main channel under both ecological conditions. The temporal and spatial distribution patterns of the fish species composition and abundance were clearly different before the habitat loss and after, during the natural recovery. “Before” the collapse the main channel and seagrass beds showed significant differences between the habitats, on the contrary, during the natural recovery it was not possible to distinguish both communities, which were much similar to those of the non-vegetated areas in the 1980s. Generally, fish communities of Z. noltii seagrass beds in the 1980s were more rich and diverse and with higher abundance of individuals. Apparently, disappearance of Z. noltii seagrass beds led to the disappearance or decrease in abundance of resident fish species in that habitat, which have not return to the system or recover the respective populations even after the beginning of the recovery of Z. noltii seagrass beds. This study also revealed that this system has registered an increased colonization from species with subtropical affinity, which might be related to gradual temperature increase at a global scale. However, modifications due to the collapse and recovery of the Z. noltii seagrass beds seemed to surpass the effects resulting from climate changes ; N/A