Trees hold the lifeline of the earth's biodiversity and serve as a commercial entity delivering broad applications to humankind. In addition to being used as wood and timber, trees are a source of secondary metabolites, medicinal compounds, and other derivatives with high commercial value. Thus, the scope for improvement of these traits and quality traits (insect/pest resistance, wood quality, etc.) has always been demanding; however, limited progress has been made compared to other crop species. Trait improvement has always been challenging in trees owing to several practical difficulties, but genomics has enabled the precise identification of genetic determinants of these traits and provided tools and approaches to tweak them for enhancing the traits of interest. Next-generation sequencing (NGS) has expedited genomics and transcriptomics research by facilitating the sequencing of genomes and transcriptomes, identifying genes, profiling the regulation of their expression, and constructing gene regulatory networks. Also, NGS has enabled the development of large-scale genome-wide molecular markers for high-throughput genotyping applications, which are useful in breeding for desirable traits. As it allows improved understanding of the gene function and its network at different developmental stages of trees with reference to an environmental stimulus can further help the breeder to enhance the knowledge on spanning genotype and phenotype. Thus, the potential of genomics in expediting trait improvement has been well realized; however, its application in tree species, particularly in commercially important ones including Tectona grandis, Azadirachta indica, Casuarina spp., and Salix spp, requires further research. Given this, the present review enumerates the progress made in genomics research on these four species and provides the roadmap for their trait improvement toward enhancing productivity and ecosystem services.