Species of Fusarium and other fungi were isolated from soybean seeds, causing complete discoloration of seed coat; a reddish discolora­tion (including both dark and light red). There was no evidence that the infections by Phomopsis sp. or Fusarium spp. were preceded by Peronos­pora manshurica. Fusarium oxysporum, F.accuminatum, Egraminearum and Phomopsis spp. These fungi were the most predominant pathogens isolated from both dark or lightly discolored seeds, in surface disinfested or non disinfested seeds. Both deoxynivalenol (DON) and HT-2 toxins were present in dis­colored seeds. The extensively discolored red seeds contained the larg­est amount of the toxin, with the highest concentration localized in the seed coats. Germination of the reddish discolored seeds and iodine number were decreased. There was an increase in the free fatty acids contents, and a little change in total oil and protein content, while only meal color was deleteriously affected.