Many syngnathids are threatened and endangered due to habitat loss and modification as well as over harvesting for the aquarium trade. There are several syngnathid species that live permanently in seagrass and are dependent on it throughout their life cycle, and the global decline in seagrass is a substantial concern for these species. The alga Caulerpa taxifolia is a nuisance algal species in Moreton Bay and many areas that were once seagrass beds have now been colonized by C. taxifolia. This loss in seagrass habitat poses a direct threat to syngnathid populations in Moreton Bay. Habitat surveys found that syngnathids were absent from C. taxifolia beds, but did occur in adjacent seagrass beds. The objective of this study was to examine possible mechanisms driving differences in abundance between habitat types. Specifically, we examined habitat structure and chemical cues between unvegetated, C. taxifolia, and seagrass habitats (Zostera muelleri and Halophila spinulosa). We found that the presence of any vegetated habitat was the greatest explanatory variable in all experiments, regardless of vegetation type. Further work is needed to examine additional potential mechanisms driving differential habitat abundance, in particular fine scale water movement and feeding studies.