Mexico is a major center of evolutionary radiation for the genus Quercus, with oak species occurring across different habitat types and showing a wide variation in morphology and growth form. Despite representing about 20% of Mexican species, scrub oaks have received little attention and even basic aspects of their taxonomy and geographic distribution remain unresolved. In this study, we analyzed the morphological and climatic niche differentiation of scrub oak populations forming a complex constituted by six named species, Quercus cordifolia, Quercus frutex, Quercus intricata, Quercus microphylla, Quercus repanda, Quercus striatula and a distinct morphotype of Q. striatula identified during field and herbarium work (hereafter named Q. striatula II). Samples were obtained from 35 sites covering the geographic distribution of the complex in northern and central Mexico. Morphological differentiation was analyzed through geometric morphometrics of leaf shape and quantification of trichome traits. Our results indicated the presence of two main morphological groups with geographic concordance. The first was formed by Q. frutex, Q. microphylla, Q. repanda and Q. striatula, distributed in the Trans-Mexican Volcanic Belt, the Sierra Madre Occidental and a little portion of the south of the Mexican Altiplano (MA). The second group consists of Q. cordifola, Q. intricata and Q. striatula II, found in the Sierra Madre Oriental and the MA. Therefore, our evidence supports the distinctness of the Q. striatula II morphotype, indicating the need for a taxonomic revision. Within the two groups, morphological differentiation among taxa varied from very clear to low or inexistent (i.e. Q. microphylla-Q. striatula and Q. cordifolia-Q. striatula II) but niche comparisons revealed significant niche differentiation in all pairwise comparisons, highlighting the relevance of integrative approaches for the taxonomic resolution of complicated groups such as the one studied here.