Two formerly broadly distributed woody Atriplex species now occur as fragmented populations across a range of microhabitats in the San Joaquin Valley Desert, southern California. We hypothesized that A. lentiformis and A. polycarpa exhibit inter- and intra-specific differences in their leaf and stem structural and functional traits corresponding with differences in soil salinity and aridity. Water potential, xylem structure and function and leaf traits were compared between three populations of A. lentiformis and four populations of A. polycarpa. The two species significantly differed in their xylem traits, with A. lentiformis displaying lower xylem density, wider mean and maximum vessel diameters and higher hydraulic conductivity (Ks). They also differed in their leaf traits, such that A. lentiformis had larger leaves with higher specific leaf area (SLA) than A. polycarpa. Significant intra-specific differences occurred among leaf traits (leaf area, SLA) in A. lentiformis populations. In contrast, populations varied in their stem xylem structural traits (mean vessel wall thickness, mean vessel diameter, maximum vessel length) among A. polycarpa populations. Many of these differences were associated with soil salinity in A. lentiformis, and with minimum seasonal water potential in A. polycarpa. Overall, both saltbush species showed high intra- and inter-specific trait variation. This could be a critical consideration in understanding the evolution of these native species and has important implications for their conservation and restoration.