Lint yield of cotton, particularly Pima (Gossypium barbadense) can be reduced by high temperatures during peak flowering periods in irrigated Southwestern conditions. High stomatal conductance (GS) may confer adaptive advantage to genotypes that experience supra-optimum temperatures by its association with elevated leaf cooling to reduce canopy temperatures (1). Interspecific differences for GS has been well established. The objective of this research was to practice divergent selection for GS in a population derived from G. hirsutum X G. barbadense introgression (TM1 X NM24016). TM1 is a typical G. hirsutum and NM24016 (2) is a introgressed line derived from G. hirsutum X G. barbadense hybridization program. Divergent selection for GS was practiced on the F2.3 generation in Maricopa, AZ in 1996. DNA was isolated from all 118 F2 plants in 1995 for genetic mapping experiments and QTL analysis of GS. Replicated field experiments of selected F2.4 progeny (10 high GS and 10 low GS) were grown in Maricopa, AZ and Las Cruces, NM in 1997. GS was measured at both locations at peak flowering as described by Radin et al. (3). Based on F3 and F4 data the realized H for GS was estimated to be 0.41 in Maricopa. This is reflected in the significant difference between the mean of the high GS F2.4 lines (n=10) 552 mmol m-2 s-1 and the low GS lines (n=10) 457 mmol m-2 s-1 at Maricopa in 1997. The difference at Las Cruces was non-significant (314 for high GS vs 282 for low GS). The absence of supraoptimum temperature at Las Cruces relative to Maricopa probably explains this difference. Correlated response in lint yield was observed in Maricopa but not Las Cruces. The high GS lines were significantly higher yielding than the low GS lines at Maricopa even though the only selection has been for GS. Composite Interval Analysis was conducted on the F2.3 progeny in Maricopa utilizing DNA markers (RAPDs and SSRs). Two QTLs (LOD = 2.0 and 3.8) were detected for GS at Maricopa. These QTLs explained about 12% of the variation in the trait. Both intervals were from NM24016 and negatively affected GS. It is suspected, but not yet verified, that these regions are derived from G. barbadense. This is one of the first physiological traits that have been subjected to QTL analysis. GS is a heritable trait and seems to be significantly associated with lint yield in heat stress environments.