White’s seahorse, Hippocampus whitei, is an endangered seahorse species endemic to eastern Australia. Populations of H. whitei have declined significantly, primarily attributed to the decline of critical habitats. Effective management and conservation of threatened species should aim to address the cause of decline. In order to address the impacts of habitat loss upon a threatened species, a comprehensive understanding of the species’ habitat use is necessary, and all life stages must be considered. The study presented here aimed to determine the habitat preference of juvenile H. whitei at two age classes (2-3 months old and 5-6 months old). Habitat preference was assessed in a controlled laboratory experiment, where seahorses were offered the selection of three natural and one artificial habitat type common within Sydney Harbour, Australia.This study found an ontogenetic shift in habitat preference of juvenile H. whitei; 2-3 month old seahorses preferred the brown macroalgae Sargassum spp. (53.9 % of habitat selections), whereas seahorses aged 5-6 months old preferred artificial netting (49.25 % of habitat selections) and the seagrass Posidonia australis (40.30 % of habitat selections). Effective management and conservation of this Endangered seahorse species must consider the protection or provision of different habitats to effectively promote recovery.