Southern Ocean Island systems sustain phytoplankton blooms induced by natural iron fertilization that are important for the uptake of atmospheric carbon dioxide and serve as analogues for past and future climate change. We present data on diatom flux assemblages and the biogeochemical properties of sinking particles to explain the enhanced particulate organic carbon (POC) export fluxes observed in response to natural iron supply in the Crozet Islands region (CROZeX). Moored deep‐ocean sediment traps (>2000 m) were located beneath a naturally fertilized island bloom and beneath an adjacent High Nutrient Low Chlorophyll (HNLC) control site. Deep‐ocean carbon flux from the naturally‐fertilized bloom area was tightly correlated (R = 0.83, n = 12, P < 0.0006) with the resting spore flux of a single island‐associated diatom species,Eucampia antarctica var. antarctica. The unusually well preserved state of the Eucampia‐associated carbon flux, determined by amino acid studies of organic matter degradation, was likely influenced by their ecology, since diatom resting spores are adapted to settle rapidly out of the surface ocean preserving viable cells. The naturally fertilized bloom enhanced carbon flux and the resulting Si/C and Si/N ratios were 2.0–3.4‐fold and 2.2–3.5‐fold lower than those measured in the adjacent HNLC control area. The enhanced carbon export and distinctive stoichiometry observed in naturally fertilized systems is therefore largely not attributable to iron relief of open ocean diatoms, but rather to the advection and growth of diatom species characteristic of island systems and the subsequent flux of resting spores. Carbon export estimates from current natural iron fertilization studies therefore represent a highly specific response of the island systems chosen as natural laboratories and may not be appropriate analogues for the larger Southern Ocean response. The broader implications of our results emphasize the role of phytoplankton diversity and ecology and highlight the need for a species‐centered approach in order to understand the regulation of biogeochemical fluxes.