Frankliniella fusca (Hinds) (Thysanoptera: Thripidae) is an early-season cotton pest. Seedlings are injured by larvae, which hatch from eggs oviposited into seedlings and feed on developing plant tissue. Better understanding F. fusca oviposition in cotton may improve their management and address new challenges such as resistance to neonicotinoid seed treatments (NSTs). Cotton seedlings exposed to F. fusca were either cleared and stained to determine egg density and location, or dissected and washed to determine larval distribution. Experiments were conducted in the greenhouse with a susceptible population and field with a NST-resistant population. Eggs of both populations were recovered predominantly in cotyledons. Larvae were more uniformly distributed on seedlings. On NST seedlings, oviposition by the susceptible population was reduced and preference shifted to true leaves. NSTs did not alter egg placement by the resistant population.These findings suggest that injury to cotton seedlings is primarily caused by F. fusca emerging on the cotyledons, and then moving to developing leaves. The oviposition shift in NST plants correlates with how systemic NSTs have been reported to concentrate in cotyledons. This can better inform management tactics in cotton, such as well-timed foliar sprays, which, given the current resistance issue, are needed to maintain effective thrips management.