Sustainable vegetable production is mainly based on strong linkages among horticulturists, plant breeders, biotechnologists, and other stakeholders. Molecular markers, genome sequencing, gene editing, genetic transformation, and tissue culture are efficient biotechnological tools that are assumed to be useful for plant breeders for crop improvement purposes. Biotechnological approaches have the potential to improve tolerance in the vegetables growing under biotic and abiotic stresses. Since morphological and biochemical markers are highly affected by environmental influences, their applications have been very limited. Many molecular markers and sequencing techniques are regularly utilized in phylogenetic studies, evaluation of genetic variability and evolutionary relationships, precise taxonomy-based classification, identification of diverse germplasm, and high-yielding hybrids. Further, various biotechnological tools are being used to identify desired and undesirable attributes that are regulated by numerous genes. Over the past 20 years, many plant species have been successfully characterized by using these well-established molecular techniques. Recent molecular marker approaches provide an improved genotypic platform for the development of high-yielding cultivars. The present study explores deep insights into several molecular markers, functional genomics, genome editing, and genetic transformation approaches that have been used for numerous genomic analyses of vegetable crops. CRISPR/Cas-based genome editing tools are now widely used in vegetable crops. The current review validates the adoption of molecular technologies for genome identification, sequencing, editing, transformation, re-sequencing, barcoding, and QTLs mapping. Diverse genotypes can be identified and further utilized for the development of high-yielding germplasm with resilience to biotic and abiotic challenges.