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Previous studies of the desert shrub Encelia farinosa have shown variation of morpholological and physiological integration that appears to match environmental differences among populations. Such findings led us to ask if there is a genetic basis for such differentiation that may be related to physiological control of intercellular CO2 concentrations as indicated by carbon isotope discrimination (Delta) values, and if genetic variance for Delta is detectable within populations. Under common environment conditions, Delta values were compared between two populations of E. farinosa from desert regions with contrasting rainfall patterns: Superior, Ariz., a region with high annual rainfall and droughts of short duration, and Oatman, Ariz. a region with lower annual rainfall and longer drought periods. Superior plants had consistently greater mean Delta values than Oatman plants across a broad range of soil water potentials, indicating that there is a genetic basis for Delta variation between these populations. At the intrapopulation level only Oatman plants showed detectable genetic variance of Delta based on: (1) consistent individual-rank values for Delta among soil-drought stages, and (2) evidence of heritable genetic variance for Delta during one drought stage. No genetic variance in Delta was evident for the Superior population. It is hypothesized that the high spatio-temporal heterogeneity of water availability at Oatman may facilitate the maintenance of genetic variance for carbon isotope discrimination within this population. Both the inter- and intra-population level findings suggest that selection associated with rainfall and drought has resulted in genetic divergence of the physiological factors involved in Delta determination for these populations. There appears to be strong differences of water-use and carbon-gain strategies among populations, and broader functional breadth among plants in the habitat of greatest environmental heterogeneity.