Found at depths of at least 6 m. H. histrix is often associated with sponges and sea-squirts, or is found in areas of sparse or no seagrass (R.H. Kuiter in Lourie et al. 1999). The species primarily lives at moderate depths of about 15 m or deeper, on soft bottom with soft corals and sponges, but it is occasionally found inhabiting shallower algae-rubble reef zones in about 10 m depth (Kuiter 2000).

This species may be particularly susceptible to decline. All seahorse species have vital parental care, and in many species studied to date have high site fidelity (Perante et al. 2002, Vincent et al. in review), highly structured social behaviour (Vincent and Sadler 1995) and relatively sparse distributions (Lourie et al. 1999). The importance of life history parameters in determining response to exploitation has been demonstrated for a number of species (Jennings et al. 1998).