The aim of this study was to determine and compare habitat preferences for male and female adult and juvenile White's seahorse Hippocampus whitei and assess their movements and site fidelity over 4 years. Data were collected from three sites along 1·5 km of estuarine shoreline in Port Stephens, New South Wales, Australia, from 2006 to 2009 using H. whitei that had been tagged with visible implant fluorescent elastomer. Relative availability of 12 habitats and habitat preferences of H. whitei was determined, based on the habitat that H. whitei used as a holdfast. Hippocampus whitei occurred in nine different habitats; adults preferred sponge and soft coral Dendronephthya australis habitats with no difference between male and female habitat preferences whilst juveniles preferred gorgonian Euplexaura sp. habitat. There was a significant preference by adults for D. australis colonies with height >40 cm and avoidance of colonies <20 cm. Neither adults nor juveniles used sand or the seagrasses Zostera muelleri subsp. capricorni and Halophila ovalis. Hippocampus whitei showed cryptic behaviour with c. 50% of adult sightings cryptic and c. 75% for juveniles with crypsis occurring predominantly in Sargassum sp. for adults and Euplexaura sp. habitat for juveniles. Within sites, females moved significantly longer distances (maximum of 70 m) than males (maximum of 38 m) over 20 months. Strong site fidelity was displayed by H. whitei with males persisting at the same site for up to 56 months and females for 49 months and no H. whitei moved between sites. The longest period that an H. whitei was recorded on the same holdfast was 17 months for a male and 10 months for a female. As this species displays strong site fidelity, specific habitat preferences and has a limited distribution, future management needs to minimize the risk of habitat disturbance as loss of key habitats could have a negative effect on species abundance and distribution.