Single nucleotide polymorphisms (SNPs) are the most frequent source of genetic variation in eukaryotic species. Having access to well-distributed SNPs across the genome, segregating between and within the diversity groups of each species, is key to genetic studies and applications. Recently, we took advantage of the advances in second-generation sequencing technologies and the development of bioinformatics tools to characterise genetic diversity panels in pea and faba bean, two grain legume species with large genomes (4.45Gb and 13Gb, respectively). We chose a target capture technology focusing on coding regions only because whole-genome resequencing is relatively expensive for species with large genomes and because polymorphisms capture in repetitive non-coding regions is difficult to achieve or to interpret. We generated exome-enriched genomic libraries for 240 and 248 pea and faba bean accessions, respectively. After paired-end Illumina sequencing, the reads were mapped to the latest pea and faba bean genome assemblies, allowing the discovery of approximately 2.2 and 1.75 million robust SNPs in the two panels, respectively. The development of these SNP resources paves the way for a wide range of applications requiring low, medium or high marker density. These data can be used directly to set up genome-wide association studies using the sequenced panels in both species, as has already been demonstrated for aphid resistance in pea. They can also be used for the exploitation of genetic resources and for marker- and genomic-assisted selection. Here, we show how the pea and faba bean research and breeding communities can benefit from recent developments, and we highlight the importance of common tailored genotyping tools that can be developed based on the available SNP sets. We also discuss the importance of identifying and incorporating functional markers related to traits of interest including biotic and abiotic stress resistance and seed and protein quality.