The infaunal living clypeasteroid echinoid genus Echinocyamus is considered a model organism for various ecological and paleontological studies since its distribution ranges from the polar regions to the tropics, and from shallow-marine settings to the deep-sea. Deep-sea analyses of this genus are rare, but imperative for the understanding and function of these important ecosystems. During the 2012 Southern Surveyor expedition, 35 seamounts off the east coast of Australia were dredged in depths greater than 800 m. Of these, six dredges contained a total of 18 deep-sea Echinocyamus tests. The tests have been analyzed for taphonomic alterations including abrasion patterns, macro-borings, micro-borings, depressions on the test, test staining, test filling, encrustation, and fragmentation. Findings are interpreted in the context of the deep-sea setting and are compared to Echinocyamus samples from shallow-water environments. Results show that abrasion in deep-sea environments is generally high, especially in ambulacral and genital pores indicating that tests can persist for a long time on the seafloor. This contrasts with shallow-water Echinocyamus that show lower abrasion due to early test destruction. Macro-borings are present as single or paired holes with straight vertical profiles resembling Lithophaga borings. Micro-borings are abundant and most likely the result of sponge or fungal activity. Depressions on the tests, such as scars or pits, are likely the result of trauma or malformation during ontogeny. Test staining is common, but variable, and is associated with FE/Mn oxidation and authigenic clays based on elemental analyses. Test filling occurs as loose or lithified sediment. Encrustation is present in the form of rudimentary crusts and biofilms. No macro-organisms were found on the tests. Biofilm composition differs from shallow-water environments in that organisms captured in the biofilm reflect aphotic conditions or sedimentation of particles from higher in the water column (e.g., coccoliths). Fragmentation is restricted to the apical system and pore regions. Results of this first comparative study on deep-sea Echinocyamus from Australian seamounts show that the minute tests can survive for a long time in these settings and undergo environmental specific taphonomic processes reflected in various taphonomic alterations.