Onion Maggot

Delia antiqua

This small fly is a relative of the Cabbage Maggot/Fly and can be a serious problem for onion growers in the northern half of the country (it also attacks leek, shallot and garlic). Like the Cabbage Fly it lays its eggs at the base of a plant and the newly hatched larvae burrow down into the root or bulb. The larvae will kill a small seedling and then move on to other seedlings (one larvae may kill up to a dozen seedlings). A larger plant won’t necessarily die, but it will be stunted in growth and the lesions they create may allow rot causing organisms to enter). Later generations may infest mature bulbs. 

Row covers are an effective control. You should remove all onions from the ground to reduce the chances of it overwintering (it overwinters as a brown pupa which looks like a grain of wheat). Another strategy is to plant some onion sets as a trap crop near your seedlings (and then remove them). Red Onions may be less susceptible.