In this study, new single nucleotide polymorphism (SNP) markers were developed for common bean (Phaseolus vulgaris L.) and related Phaseolus species. The applied strategy presents new and interesting aspects, such as the choice of accessions used, which was aimed at capturing a large portion of the genetic diversity present in the common bean, with particular focus on wild and domesticated materials from Mesoamerica and the identification of loci for sequencing. Indeed, the primer pairs for 34 loci were designed with the main strategy being to search for single-copy orthologous genes among the legumes (for use in other legume species and comparative analyses). The 10 remaining loci were selected as being near to domestication quantitative trait loci or detected as putatively under selection during domestication in previous studies. To provide an efficient and inexpensive genotyping platform for geneticists and breeders, we used sequence data to develop 60 new SNP markers for KASPar assay genotyping. The same sample was also genotyped with SNP markers developed for common bean in other studies for the same assay. This allowed testing for systematic bias according to the criteria chosen to select the genotypes in which the genetic diversity is surveyed during SNP discovery. Finally, we show that most of the SNP markers worked well in a set of accessions of other species belonging to the Phaseolus genus. The genetic resources developed will be very useful not only for breeding, but also for biodiversity conservation management and evolutionary studies on legumes.