Recently, the flies are used to pollinate onion for seed production in Korea. However, the use of flies for pollination has caused complaints by local residents in onion seed production owing to sanitation issues and smell. Therefore, we studied the effects of pollination with bumblebee (Bombus terrestris) and flies(e.g., houseflies, flesh flies, blue bottle flies and blowflies) at small net(1.8m×2.3m×1.8m) in the greenhouse(66m2) for onion seed production. Although the number of flies was about 70 times than number of bumblebee workers, flies and bumblebees showed equivalent pollination efficiency. Therefore, pollination by B. terrestris can be used as an alternative approach in seed production of onion. An analysis of the most appropriate colony of B. terrestris for seed production of onion in small net showed that colony composed of fifty to eighty workers per small net was the most efficient level. When early maturing onion cultivars ‘Salad-5’ and ‘Yeonsinwhang’, and mid-late maturing onion cultivar ‘Colossus’ were pollinated by B. terrestris and files in small net, B. terrestris showed rather efficient pollination efficiency than flies or was equivalent to flies. In addition, difference among onion cultivars was affecting pollination effect by flies but was not affecting pollination effect by B.terrestris.