Meta-omics refers to the integrated analysis of multiple “omics” data layers (such as genomics, transcriptomics, proteomics, metabolomics) across different biological systems. When applied to crop improvement, meta-omics provides a holistic view of plant biology, allowing researchers to identify new ways to enhance crop productivity, resilience, and nutritional quality. Besides, the amalgamation of meta-omics with omics approaches provides valuable insights into the molecular mechanisms underlying important traits in horticultural crops, flowers, including disease resistance, fragrance, color, shelf-life, and environmental adaptability. These technologies enable the identification of key genes, proteins, and metabolites, facilitating the development of molecular markers for selective breeding, genome editing, and stress management strategies. The application of meta-omics in horticulture holds promise for accelerating the breeding of superior varieties, improving post-harvest management, and ensuring sustainable production practices. This chapter explores the prospects and applications of meta-omics in horticulture and coupled with omics in commercial flowers, highlighting current innovations and future directions for integrating omics tools in the global horticulture industry. By leveraging these technologies, the horticulture sector can address emerging challenges and meet the growing demands for high-quality, disease-resistant, and environmentally sustainable production.