A cross-basin (longitudinal) study of lanternfishes in the southern Tasman Sea abyssal basin during the austral winter of 2008 and 2009 found that mean biomass in the Western sector was higher than that in the Eastern sector, corresponding with cross-basin patterns in oceanographic heterogeneity and productivity. Dominant species over the abyssal basin differed from those previously recorded over the neighbouring continental slope. Vertical biomass profiles indicated diffuse night-time distributions in the Central sector and extensive diel vertical migrations in the Eastern sector. In the Western sector, macrocrustacean δ 13 C values were significantly higher, and δ 15 N significantly lower, than those in the Eastern sector. The results indicate a cross-basin difference in the primary productivity environment and 15 N enrichment at the base of the foodweb. The cross-basin pattern in lanternfish δ 15 N values mirrored that for macrocrustaceans and was not correlated with standard length. Lanternfish δ 13 C values did not differ between sectors, but there were depth-wise differences, with values in the shallowest stratum (0–200m) significantly higher than those in the deepest stratum (800–1000m). Calculated trophic levels (TLs) of lanternfishes spanned the third trophic level and marked niche segregation was evident in the Eastern (mean TL 3.0–3.9) and Central (mean TL 2.5–3.6) sectors. Together, the results suggest that the Eastern and Western sectors are distinct sub-basin scale pelagic habitats, with implications for ecosystem modelling and future monitoring.