Micronekton distributions and assemblages were investigated at two shallow seamounts of the south-western Indian Ocean using a combination of trawl data and multi-frequency acoustic visualisation techniques. La Pérouse (∼60 m) seamount is located on the outskirts of the oligotrophic Indian South Subtropical Gyre province with weak mesoscale activities and low primary productivity all year round. The “MAD-Ridge” seamount (thus termed in this study; ∼240 m) is located in the productive East African Coastal (EAFR) province with high mesoscale activities to the south of Madagascar. This resulted in higher micronekton species richness at MAD-Ridge compared to La Pérouse. Resulting productivity at MAD-Ridge seamount was likely due to the action of mesoscale eddies advecting larvae and productivity from the Madagascar shelf rather than local dynamic processes such as Taylor column formation. Mean micronekton abundance/biomass, as estimated from mesopelagic trawl catches, were lower over the summit compared to the vicinity of the seamounts, due to net selectivity and catchability and depth gradient on micronekton assemblages. Mean acoustic densities in the night shallow scattering layer (SSL: 10-200 m) over the summit were not significantly different compared to the vicinity (within 14 nautical miles) of MAD-Ridge. At La Pérouse and MAD-Ridge, the night and day SSL were dominated by common diel vertical migrant and non-migrant micronekton species respectively. While seamount-associated mesopelagic fishes such as Diaphus suborbitalis (La Pérouse and MAD-Ridge) and Benthosema fibulatum performed diel vertical migrations (DVM) along the seamounts’ flanks, seamount-resident benthopelagic fishes, including Cookeolus japonicus (MAD-Ridge), were aggregated over MAD-Ridge summit both during the day and night. Before sunrise, mid-water migrants initiated the first vertical migration event from the intermediate to the deep scattering layer (DSL, La Pérouse: 500-650m; MAD-Ridge: 400-700 m) or deeper. During sunrise, the other taxa contributing to the night SSL exhibited a successive series of vertical migration events from the surface to the DSL or deeper. Some scatterers were blocked in their upward and downward migrations due to the seamount topography, more commonly known as the sound scattering layer interception/topographic blockage hypothesis. Possible mechanisms leading to the observed patterns in micronekton vertical and horizontal distributions are discussed. This study contributes to a better understanding of how seamounts influence the diel vertical migration, horizontal distribution and community composition of micronekton and seamount-associated/resident species at two poorly studied shallow topographic features in the south-western Indian Ocean.