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We tested the effects of hybridization and introgression on the levels of leaf fluctuating asymmetry (FA) in a hybrid zone between Quercus magnoliifolia and Quercus resinosa at the Tequila volcano, Jalisco state, Mexico, in which the species are distributed along an altitudinal gradient ranging from 1400 to 2100 m. Bayesian clustering analysis was performed with STRUCTURE on data for eight nuclear microsatellite loci to assign individuals from reference populations and from the hybrid zone to pure or hybrid genotypic classes. To test the performance of the assignment procedure and to determine optimal thresholds for genetic assignment pure, hybrid and backcrossed genotypes were simulated (from the allelic frequencies found in real pure populations of the two species) and reanalyzed with STRUCTURE. Leaf FA and morphological identification of parental and hybrid individuals were obtained using geometric morphometric techniques. We found genetic and morphological evidence of a hybrid zone by secondary contact at the Tequila volcano. The genotypes and phenotypes were significantly correlated with altitude along the mountain, but no correlation between them was found. FA was higher in F1 hybrids and backcrossed genotypes than in pure species. Levels of FA were more correlated with the proportion of genetic ancestry of each individual than with leaf morphology or altitude, supporting the hypothesis that hybridization is associated with development instability potentially caused by disruption of coadapted gene complexes characteristic of each species. [ABSTRACT FROM AUTHOR]