We observed high cell numbers of large (>50μm) nitrogen-fixing phytoplankton to the south and east of Madagascar in February 2005. The distribution of the nitrogen-fixing (diazotrophic) taxa found was markedly different: Trichodesmium was most abundant (500–1000 trichomes L⁻¹) in the waters at the southern tip of Madagascar; while high numbers of diazotrophic diatoms (125–500 cells L⁻¹) were limited to the southeast of Madagascar. Using literature values of nitrogen-fixation per cell, we estimate potential rates of nitrogen-fixation for Trichodesmium (south of Madagascar) of 1–5 mmol N m⁻² d⁻¹ and for diazotrophic diatoms (east of Madagascar) of 0.4–2.4 mmol N m⁻² d⁻¹. These cell-based estimates highlight the potential for significant nitrogen-fixation in the southwest Indian Ocean. High numbers of diazotrophic diatoms in subtropical waters to the east of Madagascar may have important implications for the biogeochemistry of the austral phytoplankton bloom in this region.