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Viruses are an important disease source for beans. In order to evaluate the impact of virus disease on <i>Phaseolus</i> biodiversity, we determined the identity and distribution of viruses infecting wild and domesticated <i>Phaseolus</i> spp. in the Mesoamerican Center of Domestication (MCD) and the western state of Nayarit, Mexico. We used small RNA sequencing and assembly to identify complete or near-complete sequences of forty-seven genomes belonging to nine viral species of five genera, as well as partial sequences of two putative new endornaviruses and five badnavirus- and pararetrovirus-like sequences. The prevalence of viruses in domesticated beans was significantly higher than in wild beans (97% vs. 19%; <i>p</i> < 0.001), and all samples from domesticated beans were positive for at least one virus species. In contrast, no viruses were detected in 80–83% of the samples from wild beans. The <i>Bean common mosaic virus</i> and <i>Bean common mosaic necrosis virus</i> were the most prevalent viruses in wild and domesticated beans. Nevertheless, <i>Cowpea mild mottle virus</i>, transmitted by the whitefly <i>Bemisia tabaci</i>, has the potential to emerge as an important pathogen because it is both seed-borne and a non-persistently transmitted virus. Our results provide insights into the distribution of viruses in cultivated and wild <i>Phaseolus</i> spp. and will be useful for the identification of emerging viruses and the development of strategies for bean viral disease management in a center of diversity.