Recently, biomolecular and genomic techniques have experienced a tremendous development, which has enormously accelerated genetic research. This progress has expanded the application of genomics to non-model species of agricultural and horticultural importance. Thus, the recent increase in vegetable production worldwide can be also ascribed to the application of innovative genetic and genomic tools to plant breeding. Improvements of these tools and integration of genomics, biotechnologies and bioinformatics with conventional methods of plant breeding is expected to further contribute to increasing food quality and safety and crop yields while reducing costs and protecting the environment. This paper gives an overview of the most recent advances in the development of genetic and genomic resources and of technological platforms available for plant breeding, giving examples of the latest results deriving from their application to vegetable crops. The use of modern genomic and molecular genetic tools has allowed the combination of molecular and morphological data for the identification of accessions, the analysis of phylogenetic relationships and the study of evolutionary processes and speciation. The integration of molecular analysis with morphological evaluation of accessions has been especially successful in the classification of complex genera with controversial taxonomy. In some cases, previously accepted phylogenetic relationships were not confirmed by large-scale analysis of germplasm collections with highly informative molecular markers. Molecular markers are also extremely useful for fingerprinting, allowing unambiguous identification of plant genotypes. Recent developments of high-throughput technological platforms for DNA marker analysis has provided large automation and cost containment, making traceability and genetic identity certification of vegetable genotypes feasible throughout the food chain. This application is especially relevant for the commercial valorisation of the superior quality of Italian vegetable crops and their products and for addressing consumer concerns for food safety and quality. Many high-density genetic and physical maps have been recently developed for vegetable species, together with other genomic platforms such as EST data bases, saturated or nearly-saturated mutant collections, microarrays and bioinformatic tools. This wealth of resources for structural and functional genomics finds its application in evolutionary studies, identification of genes responsible of phenotypic variation, genomic sequencing etc. and in general in genetic improvement of the species for which they were developed, but are also invaluable for related species. The above genomic approaches are allowing the identification of genes and Quantitative Trait Loci responsible for relevant traits and their localisation on high-density genetic maps. Hence, selection of improved genotypes is now possible with an unprecedented efficiency through marker assisted breeding. The exploitation of the very large number of favourable alleles identified through genetics and genomics is often hindered by reproductive barriers. Examples are given of modern biotechnology tools for overcoming these barriers, increasing genetic variability and producing new improved varieties. Case studies are presented of the integration of conventional breeding with biomolecular technologies and genomics for the improvement of vegetable crops for important traits. The tremendous progress of genomic technologies holds premises for the large scale application of genomics-assisted breeding in a near future.