Abstract : 'Northern Hardwoods,' are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate forest management practice decisions. Genetic tools, such as microsatellite markers developed using next generation DNA sequencing technologies, can be used to address these challenges. Here we report the development of nuclear microsatellite markers in one of the most important hardwood tree species, sugar maple (Acer saccharum Marsh.) (Chapter II). We also use genic microsatellite markers to study the introgression patterns of adaptive alleles in two interfertile red oak species, Quercus rubra and Quercus ellipsoidalis (Chapter III). Using the paired-end low coverage Illumina sequencing technology, we developed a set of seven nuclear microsatellite markers (nSSRs) in sugar maple (Acer saccharum Marsh.). Initially, we screened 96 markers in a panel of six unrelated individuals, out of which seven markers produced polymorphic PCR products. These markers were utilized to analyze genetic variation and gene flow in one sugar maple population in an urban setting consisting of 48 individuals. Additionally, 96 seeds from one open pollinated adult tree were used for the gene flow analysis. In addition to these seven markers, we also tested six previously published microsatellites. Paternity analyses displayed effective dispersal of pollen in the sugar maple population with 76% of gene flow from outside the stand. There was no fine-scale genetic structure observed in this population, which also suggested effective dispersal of both seeds and pollen. To check the transferability of these markers to other Acer species, four individuals from each species of Acer rubrum L., Acer saccharinum L., Acer platanoides L., and Acer ginnala Maxim. were tested at these markers. All markers amplified PCR products in these four species. However, only two markers, AS47 and SM37, were locus-specific and polymorphic in one species (A. ginnala). These markers can serve as an important tool to study genetic variation patterns in sugar maple populations in the face of climate change. Quercus rubra L. and Q. ellipsoidalis E. J. Hill are two interfertile red oak species with different adaptations to drought. I have studied the introgression of adaptive microsatellite alleles at a CONSTANS-Like gene (COL) as a response to micro-environment between these two hybridizing species in two sympatric populations. My results indicated that divergent selection in contrasting environments resulted in high interspecific differentiation at COL. However, interspecific differentiation was lower in sympatric stands, where both species occur in similar environments. The introgression of allele 138 from Q. ellipsoidalis into Q. rubra was higher compared to introgression of allele 141 from Q. rubra into Q. ellipsoidalis in contrast to earlier studies in parapatric populations. My results suggest that the introgression of adaptive genes between two red oak species is strongly affected by environmental selection.