Eucalyptus is an important industrial species with tolerance to drought and salt stress. Genetic improvement activities including quantitative trait loci (QTL) mapping for pulping and adventitious rooting traits are in progress, but no information is available on the genomic regions on adaptive traits such as stomatal characteristics. In this study, an interspecific cross between Eucalyptus tereticornis and E. grandis was generated for the development of genetic map and QTL identification for stomatal traits. Simple sequence repeats (SSRs), inter-simple sequence repeats (ISSRs) and sequence related amplified polymorphism (SRAP)markers were used for genotyping the F1 individuals. Parent-specific geneticmaps (female, 1023.56 cM;male, 1049.64cM) and consensus map (1049.4 cM) were developed. QTL analysis was carried out to identify the chromosomal regions affecting stomatal density, area and pore length in adaxial and abaxial leaf surface. Seven QTLs were identified with phenotypic variation of 11.36 to 27.30% for stomatal density, area and pore length. Correlation of stomatal traits when combined with growth and wood properties would have greater implications for generation of stress tolerant eucalypt hybrids with higher productivity and adaptability.