Plant hydraulic characteristics were studied in diploid, tetraploid and hexaploid cytotypes of Atriplex canescens (Chenopodiaceae) to investigate the potential physiological mechanism underlying the intraspecific habitat differentiation among plants of different ploidy levels.  Populations of A. canescens from different habitats of the Chihuahuan Desert (New Mexico, USA) were analyzed using flow cytometry to determine ploidy levels. Traits related to xylem water transport efficiency and safety against drought-induced hydraulic failure were measured in both stems and leaves.  At the stem level, cytotypes of higher ploidy levels showed consistently lower leaf-specific hydraulic conductivity but greater resistance to drought-induced loss of hydraulic conductivity. At the leaf level, comparisons in hydraulics between cytotypes did not show a consistent pattern, but exhibited high plasticity to proximal environmental conditions related to soil water availability.  The results suggest that there is a trade-off between stem hydraulic efficiency an safety across ploidy levels, which underlies the intraspecific niche differentiation among different cytotypes of A. canescens. Polyploidization is likely an important mechanism in adaptation to the environmental heterogeneity related to water availability, and variation in water-related physiology found in the present  study suggests a fundamental basis for the coexistence of different cytotypes in desert environments.