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We report the first data on the use of occasionally inundated habitats in a Mediterranean coastal lagoon by the Spanish toothcarp ( Aphanius iberus), a cyprinodontid fish in danger of extinction. During a flooding period, we sampled the fish population and the macroinvertebrate community in three contrasting habitats: mats of green algae, open water, and a habitat dominated by glasswort ( Salicornia patula) that is occasionally inundated. The three habitats displayed strong variation in density and species composition of invertebrates in the water column and the benthos. In general, algal mats had higher invertebrate biomasses, but glasswort had higher diversity of organisms, in part of terrestrial origin. The density of toothcarp was very low in the open water. The habitat that is occasionally inundated (glasswort) significantly had the highest density of mature toothcarp, while immature fish were similarly abundant in the glasswort and algal mat habitats. Condition (weight–length relationship) and total food biomass in the gut contents of immature toothcarp was significantly higher in algal mats than in glasswort, whereas there were no such differences for mature fish. Therefore, the occasionally flooded habitat (glasswort) was positively selected by large mature toothcarp but seemed a disadvantageous habitat for immature individuals. [ABSTRACT FROM AUTHOR]