Chickpea seeds entering store carry a microflora of ‘field’ and ‘storage’ fungi. Field fungi gradually disappear and storage fungi then predominate. These fungi especiallyAspergillus flavus, A. niger, A. nidulans, A. ochraceusandPenicilliumspp. grow vigorously and initiate grain spoilage and aflatoxin elaboration. The shift in mycofloral spectrum was more rapid in seeds stored in jute bags than those stored in metal bins. Moisture content and aflatoxin contamination in seeds of jute bags was maximum during Sept.‐Oct. The internal environment of metal bins is comparatively less influenced by the external conditions and initially restricts fungal growth and aflatoxin elaboration. Prolonged storage however, increases seed moisture content and aflatoxin is increased in chickpea seeds after six months storage in metal bins.