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The Andalusian toothcarp, Aphanius baeticus, is a critically endangered cyprinodontid species, with only nine known extant populations. Although not yet studied in the field, the distribution and abundance of Andalusian toothcarp are thought to be strongly influenced by interspecific interactions. We analysed the abundance and microhabitat use of Andalusian toothcarp in two water courses, one in which several other fish species occurred (sympatric site) and one hypersaline stream in which toothcarp was the only species present (allopatric site). Fish were sampled using plastic minnow traps and results were analysed separately for three size categories. Toothcarps were clearly more abundant in the allopatric population than in the sympatric one, though the difference was less apparent in the smallest size category. In coexistence with other species, toothcarp occupied shallower microhabitats, but in both sites in the absence of shelter fish selected deeper positions than in its absence. While in the sympatric site sheltered microhabitats were used predominately by small individuals, in the allopatric ones they were used by larger ones. Observed patterns strongly suggest that predation is the main mechanism involved in the differences in abundance and microhabitat use between sites. Our results confirm that the presence or absence of coexisting species is an important habitat feature for Andalusian toothcarp populations.