A field survey was conducted in Gboko and Ohimini Local Government Areas of Benue State where pepper is extensively cultivated to investigate the seed borne diseases of two Chilli pepper (Capsicum frutescens) types namely: ‘Sombo ’ and Birdeye. Naturally infected pepper seeds were extracted from pepper fruits collected from farmers ’ fields between August and October, 2011 from the two Local Government Areas (LGAs). Using agar plate method a total of 20 genera and 36 species from three classes of fungi were isolated and identified from 800 seed samples of pepper. Colletothrichum capsici, Aspergillus niger and A. flavus were the most frequently isolated fungi with 54.75%, 44.00 % and 29.75 % occurrence respectively. C. capsici/A.niger interaction had the highest occurrence of 3 % followed by A.flavus/A. niger interaction with 1.25%. Nematode/fungi association had 26.25 % occurrence on pepper seeds. Phoma spp, Humicola fuscoatra, Humicola dimorphospora, Bispora betulina, Phomopsis spp,Botryotrichum piluferum,Periconia byssoides,Coniothyrium fuckelii, Fumago spp, Septonema chaetospira and Syncephalotrichum racemosum are being reported on pepper seeds for the first time in Benue State. Detection of the seed borne fungi is important in the management of pepper diseases and can be a useful guide to strategic disease control
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