Ensuring seed quality, genetic purity, and varietal traceability have attained prime importance at a global level in the context to increase trees timber yield, biomass, resistance to biotic and abiotic factors, conservation, improved food security, and farmer’s livelihood. Identification on the basis of morphological traits is made empirical and often ambiguous due to the masking effect of genotype×environment (G × E) interaction, underscoring molecular techniques as a reliable and accurate approach. This chapter discusses the potential deployment of genomic tools, DNA-based markers in investigation of the underlying biological traits of forest seeds, and mapping its genome at global level. Recent strides in forest genetics emphasized the use of microsatellite markers like SSRs and EST-SSRs, and next-generation sequencing techniques like GBS, or SNPs for rapid assessment of hybrid and parental line seed purity. Association mapping determines the genetic loci linked with DNA markers in relation to seed quality or any other trait, specifically is difficult to propagate forestry species. This chapter also examine the applications of association mapping and genome-wide association studies (GWAS) to relate genetic loci to attributes such as seed quality, vigor, and disease resistance, particularly in difficult-to-propagate forestry species. This kind of information generated can be further followed and implemented in marker-assisted selection and breeding programmes. Addressing the issue of seed adulteration is crucial, as it can significantly impact the success of conservation programmes and economic viability of commercial trees and agroforestry species like poplars, Eucalyptus, Melia, etc. Apart from breeding, DNA fingerprinting is critical in seed certification, controlling genetic contamination, and tracing seed provenance for conservation efforts. Application of DNA fingerprinting in maintaining the genetic integrity and precisely identifying plant genotypes become vital for testing seed of forest species. Furthermore, forensic applications of DNA markers in illegal timber tracking and forest law enforcement are becoming increasingly important. The integration of molecular markers, artificial intelligence (AI), and remote sensing improves forest monitoring and sustainability initiatives. This write-up also provide a comprehensive overview of key researches, methodologies employed and implication of its findings on seed quality, traceability and ascertaining seed health in different tropical, subtropical, or temperate species. Insights into more resilient and sustainable seed production system by using molecular assays can ensure secure and prosperous future for forest biodiversity and conservation biology.