Low germination and high levels of fungal infections were found in seed of June plantings of dry beans in Honduras, Fusarium equiseti (12-62% incidence) was the dominant internally seedborne fungus of that season. October plantings showed fewer (P = 0.05) seed infections and less discoloration. Fusarium semitectum (7 to 21%) was the dominant seed microorganism. Stored seed (December to June) lost about 50% of its vigor and size without losing germination (89%). Bacillus licheniformis, with up to 37% incidence, was the dominant seed storage microorganism. Storage microorganisms included Aspergillus spp., other Bacillus spp., Penicillium spp., Chaetomium spp., Mucor spp., and Flavobacterium spp. Fusarium spp. varied in their recovery after storage. Fusarium semitectum was eliminated in storage, whereas F. equiseti increased. Levels of Fusarium spp., in recently harvested seed, and Bacillus and Aspergillus spp., in stored seed, were excellent indicators of seed quality losses in the field and storage in Honduras. Germination data alone was not a good indicator of seed quality because low vigor seed had excellent germination.