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Determining the mechanisms underlying the spatial distribution of plant species is one of the central themes in biogeography and ecology. However, we are still far from gaining a full understanding of the autecological processes needed to unravel species distribution patterns. In the current study, by comparing seedling recruitment, seedling morphological performance and biomass allocation of two Haloxylon species, we try to identify the causes of the dune/interdune distribution pattern of these two species. Our results show the soil on the dune had less nutrients but was less saline than that of the interdune; with prolonged summer drought, soil water availability was lower on the dune than on the interdune. Both species had higher densities of seedlings at every stage of recruitment in their native habitat than the adjacent habitat. The contrasting different adaptation to nutrients, salinity and soil water conditions in the seedling recruitment stage strongly determined the distribution patterns of the two species on the dune/interdune. Haloxylon persicum on the dunes had lower total dry biomass, shoot and root dry biomass, but allocated a higher percentage of its biomass to roots and possessed a higher specific root length and specific root area by phenotypic traits specialization than that of Haloxylon ammodendron on the interdune. All of these allowed H. persicum to be more adapted to water stress and nutrient shortage. The differences in morphology and allocation facilitated the ability of these two species to persist in their own environments.