Although research on habitat use and habitat selection is essential for understanding population ecology and behavior, most such zoological studies have used only general habitat categories describing main habitat features instead of using modern plant ecological approaches. Here, we analyze Testudo hermanni microhabitat use at a coastal Mediterranean site in central Italy by modeling tortoise presence/absence at three spatial scales, using a logistic regression design and quantitative vegetation and plant community analysis to reveal correlates of tortoise habitat use on a fine scale. Our analyses showed that only a few plant species among the many present, and these on a very small spatial scale, are important determinants of tortoise presence and site selection. We also find that tortoises chose a paradoxical combination of high levels of bare soil and high total vegetation cover. This suggests that these tortoises are selecting small patches of habitat in a matrix of less desirable habitat. Our findings also have important implications for habitat management, in that increasing the number of habitat patches containing the few significant plants is likely to be desirable, whereas increasing the size of such patches is probably less relevant.