Because of the narrowness of their niches, specialised species are often vulnerable because their populations suffer from fragmentation or low densities. Whatever the causes of their specialization, one might expect micro-habitat selection to be strong within the boundaries of the chosen niche to compensate for the costs linked to habitat constraints (variability of reproductive success due to high larval mortality, habitat fragmentation). We tested this hypothesis by investigating breeding site selection in the yellow-bellied toad (Bombina variegata) in the context of rock pools at riverbanks, which are supposed to be one of the pristine habitats of the species. In this species, breeding habitat use differs markedly from that of other European anurans since spawning takes place in small pools located in the close vicinity of rivers. Such pools experience high risks of drying up and flooding. By measuring 8 habitat variables at 187 rock pools along a 250 m river segment, we show a breeding habitat use based on a preference for pools with large volumes of water provided that they are devoid of alluvia, with a good exposition to sun. By ensuring longer water periods and faster development rates, large volumes and warm water probably reduce the mortality risks due to drying up (within suitable temperature range). This result contributes to understanding the process of niche conservatism (persistence of narrow range on certain dimensions of the niche), which is an important challenge in ecology and conservation biology.