The seed surface features of three Indian species of the genus Aeginetia (Orobanchaceae) was studied with the help of light microscopy and Scanning Electron Microscopy to understand the comparative morphology of the seed coat surface, and its utilization as a source of taxonomic evidence at the species level. The seeds of the three taxa show marked differences in their size, shape and surface ornamentation. Although Aeginetia pedunculata and A. sessilis show resemblances in their morphological and floral characters but differ in their seed coat sculpture. In A. indica the cells of the seed coat are alveolar and look like empty bunch of baskets with ribbed to scalariform thickenings on their lateral walls. In A. pedunculata outer tangential walls are retained but for a central ovoid depression or pore. In A. sessilis, however, the cells of the seed coat surface have a shallow depression. The micropylar end of the seed is smooth surfaced without any ornamentation. The comparative morphology of the seed coat surface in these three species of Aeginetia is discussed and its use as a source of taxonomic evidence is presented.