This study was conducted to assess the incidence of seed-borne fungi on rice seeds sourced from the major rice growing areas of SouthEastern Nigeria. The rice seeds were collected during the dry seasons between 2009 and 2010. Four hundred rice seeds randomly collected and surface sterilized by washing in 3% sodium hypochlorite and rinsed two times with sterile distilled water were placed in three circular rings inside the Petri dishes. The incubation was done one after the other for each variety from all the locations. Ten fungi species from eight genera were isolated from the rice seeds in all the rice growing areas of SouthEastern Nigeria. The fungi pathogens vary from one locality to another, as well as the frequency of occurrence. The pathogens isolated include: Fusarium moniliforme, F. solani, F. oxysporium, Aspergillus spp., Botridiploidia spp., Helminthosporium spp., Penicillium spp., Trichoconis padwickii, Curvularia oryzae and Phoma oryzae. Though, there was the presence of some seed-borne fungi in the rice seeds from the areas studied, most of the cultivars experienced up to 90% germination. But some cultivars had very low germination. IR 1416 from Arochukwu and GB90 from Arondiuzogu had less than 1% germination. This study shows that seed-borne organisms are major constraint in rice production in the SouthEastern states of Nigeria as a result of low seed germination stemmed from infestation of fungi organisms in the seeds.