Local seed systems, which supply about 99% of bean seeds in the east and central Africa regions, are progressively being supported as an alternative to facilitate the accessibility of improved bean varieties to farmers. However, these systems have been rightly or wrongly criticized for supplying substandard quality seeds. This study was carried out to assess the seed health of different seed grades from different sources of two popular Ethiopian bean varieties. Polymerase chain reaction (PCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to detect fungal and bacterial pathogens of the major bean seed-borne diseases. The ELISA test was used to assess the status of the bean common mosaic virus (BCMV). No fungal or bacterial pathogens were detected in the seeds. However, BCMV was detected in almost all sources except seed from one untrained farmer and one grain merchant. The study findings provide evidence about the capacity of the local seed system to produce and supply seed of an acceptable quality.