An experiment was carried out at Institute of Research and Training (IRT) of Hajee Mohammad Danesh Science and Technology University, Dinajpur during March to May 2016 for evaluating the effect of initial moisture content and different storage container on the quality of mustard seed. Three types of containers namely plastic container, polythene bag and gunny bag, and three levels moisture content i.e. 9.75, 12.25 and 14.30% were used as the treatment. Mustard seeds with 9.75% initial moisture level were found in good condition in respect of germination, less number of abnormal and dead seedlings, better shoot and root length, vigour index and poor fungal incidence. The highest germination percentage was observed 80.14−87.74%, while the lowest percent of abnormal seedling (8.64−12.04%) and dead seedling (3.33−8.27%) was found in the seeds stored with 9.75% initial moisture content at different storage periods. Fungal incidence was also found less in the seeds stored with 9.75% initial moisture content. Among three storage conditions, plastic container was showed the advantage for mustard seed storage compared to polythene bag and gunny bag. The seed of gunny bag was found inferior in quality for all parameters at all storage period. So, the results revealed that optimum moisture content and ideal storage condition has the greatest benefit on quality seeds. It is concluded that plastic container with 9.75% initial moisture content is the best for storing the mustard seed with higher quality.