Predator exclusion and habitat complexity factors that may affect juvenile red snapper Lutjanus campechanus habitat selection were examined in field and laboratory experiments. A significant predator exclusion effect was detected. Uncaged shell habitats showed significantly lower numbers of age 0 year red snapper, and both uncaged shell and block-shell habitats showed significantly lower numbers of age 1 year red snapper compared with caged habitats (P < 0·001). Habitat complexity also affected age 0 year red snapper, as mean abundance significantly decreased with decreased habitat complexity (P < 0·001). In the laboratory, age 0 year red snapper association with complex habitats significantly increased with exposure to a predator Gulf flounder Paralichthys albigutta (P < 0·001). This study showed that predator exclusion and habitat complexity were significant factors that affected the abundance of juvenile red snapper in nursery areas of the northern Gulf of Mexico. Predation may affect juvenile red snapper abundance directly through mortality and indirectly by influencing habitat selection.