Southern flounder off the coast of the Southeastern United States are particularly vulnerable to recruitment variability because of the complex ecological and morphological transformation that occurs early in their life history cycle. The effect of increasing temperature and development of metamorphosing larval southern flounder was investigated to test the hypothesis that temperature serves as a cue and a mechanism for recruitment of larvae to estuarine nursery grounds. Fish in early, mid and late stages of metamorphosis were observed in 4-hour long laboratory trials during which the temperature was raised from 13 to 23°C to include a range of offshore and estuarine temperatures that larvae potentially encounter. Observations consisted of recording fish location in the water column and fish swimming behavior to determine how larvae responded to warmer temperatures while advancing in their development. Experimental results contrasted with results from control trials that kept the temperature constant at 13°C, which validated the significance of the data. The major findings are that (1) early-larvae responded to warmer temperatures with an overall downward movement while late-larvae did not respond at all, (2) early-larvae were significantly more active than late-larvae, (3) behavioral changes were temperature- and stage-dependent, (4) fish location and behavior was extremely variable during metamorphosis, and (5) relative locations of early- vs. late-larvae in the artificial water column corresponded to vertical positions of larvae observed in the field. The downward shift in location of early-larvae in warmer temperatures suggests that, prior to metamorphosis, fish may facilitate their onshore transport by moving deeper in the water column. This study indicated that temperature, among other factors, affects larval flounder behavior and may serve as a cue aiding in migration into nursery areas.