Positive relationships between organismal abundance and habitat structural complexity are common in seagrasses, but the role of habitat selection in structuring these relationships (as opposed to differential mortality among habitat treatments) has been little explored. Moreover, active habitat selection may be modified by factors such as perceived predation risk or food availability, and may differ between prey and predator species. We employed mesocosms to test whether two species that are abundant in southern California eelgrass (Zostera marina) habitat, the epifaunal grass shrimp Hippolyte californiensis and the mesopredatory juvenile giant kelpfish Heterostichus rostratus, a primary predator of grass shrimp, select habitat based on structural complexity (shoot density), and if habitat selectivity is modified by predation risk and food levels. We found that juvenile giant kelpfish displayed clear preference for high complexity artificial eelgrass habitat that was not altered by predation risk or food availability, spending the majority of their time in high complexity habitat even when predators were present in high complexity habitat and food was made available only in low complexity habitat. In contrast, grass shrimp exhibited no preference for high complexity habitat in mesocosms and appeared to primarily remain on whatever habitat was initially encountered. In field experiments within naturally occurring eelgrass habitat, however, grass shrimp remained in high complexity eelgrass but fled from low complexity eelgrass regardless of predator presence. Our research highlights the important role of active habitat selection in determining species distributions in seagrass beds, the strong and overriding influence of structural complexity on habitat selection, and the importance of comparing results from controlled laboratory experiments to those from naturally occurring habitat.