The composition and spatial variability of ichthyoplankton assemblages were investigated at three shallow seamounts between latitudes 19°S and 33°S in the South West Indian Ocean (SWIO) – La Pérouse (60 m), an unnamed pinnacle south of Madagascar, referred to hereafter as MAD-Ridge (240 m), and the Walters Shoal seamount (18 m). In all, 299 larvae (23 families, 54 species) were present at La Pérouse, 964 larvae (58 families and 127 species) at MAD-Ridge, and 129 larvae (9 families, 24 species) at the Walters Shoal. Larvae of mesopelagic fish in the families Myctophidae and Gonostomatidae were the most dominant at all three seamounts. All developmental stages were present at each seamount, suggesting the larval pelagic phase of certain species occurs at the seamounts. A ‘seamount effect’ was detected only at MAD-Ridge where larval fish densities were significantly higher at summit stations. Overall, MAD-Ridge had much higher densities of fish larvae (157.0 larvae 100 m−3) than La Pérouse (31.1 larvae 100 m−3) and the Walters Shoal (9.6 larvae 100 m−3). Our study demonstrates that ichthyoplankton communities at shallow seamounts in the SWIO are more influenced by their location relative to a landmass, and to oceanographic features such as currents, mesoscale eddies and water masses than the seamount latitude and topography itself.