The relationship between altitudinal and ecological gradients has long been a dominant theme in plant ecology; moreover, how species respond to climate change has renewed this interest. Mediterranean mountains are often hotspots of endemism, and some endemic species have local distributions that span different climatic belts; hence, local variations in topography and fine-scaled niche conditions may play crucial roles in their persistence along such gradients. Studies of the fine-scaled niche are, however, very rare; most studies involve broad-scale variations in climatic parameters. The Turban lily, Lilium pomponium L. is endemic to the Maritime and Ligurian Alps, where it occurs across a wide altitudinal gradient. Previous work has shown no link between climatic marginality and geographic range limits on morphological traits and genetic variability; however, possible variations of local topographic and ecological parameters have not yet been examined. The objective of this paper is to characterise local ecological niche conditions of L. pomponium populations in the different bioclimatic zones it occupies along the altitudinal gradient. The species occurs in four main types of microecological niches. One of these niche types, with a high mineral cover, is the most abundant—type 2: it was detected in 39% of sampled quadrats and occurs across the whole bioclimatic gradient. Other niche types are more limited to subsections of the gradient: type 3 (in 19% of sampled quadrats) is restricted to high-altitude sites (>1070 m.a.s.l.) and is characterised by high vegetation and litter cover; type 4 (26%) corresponds to more forested habitats on substrates with low water retention capacities, in more inland zones close to the centre of L. pomponium distribution and across a range of altitudes; and type 1 (16% of quadrat) only occurs in the Mediterranean part of the gradient, close to distribution limits in pockets of soil among large blocks of rocks, mainly found at mid-altitudes. Despite heterogeneity in the spatial locations of niche types, there is no correspondence between ecological gradients and the distribution limits of this species. Knowledge of the fine-scaled ecological conditions that determine niche types is thus essential for conservation management of the habitats of this species and for the exploration of its possible response to ongoing climate change.