Tomatoes (Solanum lycopersicum L.) represent a valuable crop species cultivated on a global scale, with Thailand playing a notable role in Southeast Asia’s agricultural landscape. However, a comprehensive understanding of the genetic underpinnings, population dynamics, and genetic correlations among tomato cultivars within Thailand remains relatively nascent. This study conducted an extensive analysis of 283 tomato accessions sourced from Thailand’s largest germplasm repository, employing approximately 2.4 million single-nucleotide polymorphisms (SNPs) obtained through whole-genome sequencing (WGS). The results of the genetic diversity assessment demonstrate a consistent delineation of groups, as indicated by UPGMA clustering, revealing five distinct clusters, while population structure analysis unveils twelve subpopulations. These findings underscore the limited genetic reservoir within Thai tomato germplasm, providing valuable insights for germplasm management strategies and offering a promising avenue for the refinement of breeding programs aimed at enhancing tomato genetics.