Traits related to tree architecture and tolerance to abiotic stress represent innovative targets for the selection of new cultivars in the contexts of integrated fruit production (IFP) and global climatic changes. Controlling tree form and leaf functioning is thus a desirable breeding objective, but efforts have been hampered by a poor knowledge of their determinisms in apple. In the last four years, the genetic basis of architectural and ecophysiological traits was investigated in a F1 apple progeny (‘Starkrimson’ × ‘Granny Smith’ cross) of 123 genotypes. A fine phenotyping was performed over the first 3 years of growth in the open field, collecting both topological and geometrical traits along the scaffold axes and at the whole tree level. After replication of the progeny, the leaf gas exchange responses to different air droughts were studied on 1-year-old plants in a controlled environment chamber, through five increasing leaf-to-air vapour pressure deficits (VPD, from 0.5 to 3 kPa). Stomatal conductance (gsw), net CO2 assimilation (An) and transpiration (E) rates were measured, and instantaneous water use efficiency (WUE, An / E) computed. All traits were analyzed through linear models and broad sense heritability values (h²b) were estimated. A quantitative trait loci (QTL) analysis was carried out using a consensus genetic map. For each trait, QTL detection was performed on the best linear unbiased predictor (BLUP) of genotypic values, computed from the linear model. For architectural traits, high h²b values were estimated and QTLs detected for many topological and geometric traits: (i) at tree scale, surface and volume; (ii) on the trunk, mean internode length and number of sylleptic and proleptic axillary shoots; (iii) on lateral shoots, orientation, mean internode length, and number of proleptic axillary shoots. Regarding ecophysiological traits h²b values were also high, indicating a good repeatability of ecophysiological measurements in controlled conditions. QTLs were detected for gsw and E suggesting a strong genetic control of these two traits. The putative agronomic interests and potential values for selection of the architectural and ecophysiological traits are discussed