Conventional plant breeding has typically used phenotypic observations and statistical analysis to select for improved germplasm in segregating populations and the improvements in yield observed were likely due to an increase in yield potential through the unconscious pyramiding of yield-related traits. Modern breeding relies on genetics and genomics knowledge to identify superior alleles and to introduce them into new high yielding varieties and hybrids. The recent advances in genomics and the diffusion of low cost sequencing platforms have implications for both current and future plant breeding strategies. New high throughput genotyping facilities are allowing a fast identification of marker-trait associations and make possible a genome wide selection process (genomic selection). Re-sequencing projects, leading to the discovery of new alleles and new molecular breeding methods based on site specific mutagenesis in combination with the knowledge on gene functions, open new perspectives for GM and non-GM plant improvement.