Macro- and microomorphological features of Melilotus indicus complex in Egypt were examined using light and scanning electron microscopy, these includes embryo and seed characters, anatomical structure of stem and seed spermoderm. In the present study, three varieties were recorded: var. indicus, var. bonplandii and var. tommasinii. of which var. indicus is a new record to the flora of Egypt. The study revealed that morphological, anatomical and seed characters are of taxonomic significance. A key for identification of the varieties was also given.