Plant genetic resources (PGR) include cultivars, landraces, wild species closely related to cultivated varieties, breeder's elite lines and mutants. The loss of genetic diversity caused by the practice of agriculture and the availability of genetic information has resulted in a great effort dedicated to the collection of PGR. Prior to the advent of molecular profiling, accessions in germplasm collections were examined based on morphology. The development of molecular techniques now allows a more accurate analysis of large collections. Next-generation sequencing (NGS) with de novo assembly and resequencing has already provided a substantial amount of information, which warrants the coordination of existing databases and their integration into genebanks. Thus, the integration and coordination of genomic data into genebanks is very important and requires an international effort. From the determination of phenotypic traits to the application of NGS to whole genomes, every aspect of genomics will have a great impact not only on PGR conservation, but also on plant breeding programmes.