Cold seep ecosystems in the deep sea are fuelled by chemosynthetic processes based on methane emission to the sediment surface from gas hydrate disassociation, methanogenesis or thermogenic processes. While cold seep ecosystems have been studied in the last three decades worldwide, little is known about New Zealand’s cold seep habitats and associated fauna. A joint German-New Zealand cruise to the Hikurangi Margin in early 2007 enabled biological and sediment sampling to investigate the biological and sedimentological relationships and variability of seeps and their faunal diversity. Multi-disciplinary approaches were employed that included Xray radiography, stratigraphic descriptions, lebensspuren traces analysis, sediment grain size analysis, determination of total organic content, carbonate content and its stable isotopic composition, and analysis of benthic invertebrate assemblages of seep habitats. The results of this study revealed three distinctive habitats and associated fauna based on the sediment characteristics and faunal type. Habitat 1 includes all sites pertaining to Omakere Ridge, a seep-related habitat comprised of layers of very poorly sorted, sandy silt, shell hash and bands of methane-derived authigenic aragonitic carbonate nodules with low total organic content (TOC). Due to the characteristics of the sediments and death assemblages of molluscs, it is inferred that Habitat 1 methane seepage is actively diffusive, waning or dormant. Habitat 2 describes sites that are either non-seep or relic and applies to those at Bear’s Paw and Kaka. Habitat 2 constituted of shell hash overlain with very poorly sandy silt, and low carbonates content and low to medium TOC. Habitat 3 describes non-seep related habitats, and includes all sites of the Wairarapa region and one reference site from Kaka also falls into this category. Sediments for Habitat 3 constituted poorly sorted silt with high TOC and low carbonate content which can be explained by their close proximity to land and converging sea currents. The mineral components of the background siliciclastic sediments for all sites studied originated in the Tertiary mudstone of the East Coast Basin. The characteristics of seep habitats of the Hikurangi Margin were comparable to that of the Northern Hemisphere modern seep counterparts, although the abundance and distributions of seep fauna were low. Results from this research have enhanced our understanding on the spatial and variability of methane fluxes and their affects on the duration of cold seep ecosystems, especially for New Zealand. However, more such studies are essential to increase our understanding of seep sediments and explain disturbance-sediment-benthic invertebrate interactions.