The diversity of marine macrophytes of small islands in the South Western Indian Ocean region has been poorly documented and little or no information is available for the Iles Eparses (or Scattered Islands) in the Mozambique Channel. We present the first species checklist for the three largest islands of the Iles Eparses: Europa, Juan de Nova and Glorioso. Overall, with a total of 321 marine macrophyte species recorded (incl. 56% Rhodophyta, 27% Chlorophyta, 15% Phaeophyceae and 2% Magnoliophyta; Europa: 134 spp., Juan de Nova: 157 spp. and Glorioso: 170 spp.) these islands harbour 23.5% of the total species recorded for the Mozambique Channel region. We report 36 new records for the Mozambique Channel including 29 undescribed new and cryptic species. Our results highlight a decrease in species richness southward in the Channel. Because of their longitudinal arrangement between the northern and the southern ends of the Channel and their central position, Europa, Juan de Nova and Glorioso Islands represent data points of particular biogeographical interest and could be critical ‘stepping stones’ for connectivity in the highly dynamic Mozambique Channel region.