In this study a comparison between the anatomical structure of the leaves and stems of five species from the genus Heliotropium (H. ovalifolium, H. bacciferum, H. strigosum, H. supinum and H. sudanicum) in Sudan were carried out to outline the diagnostic characters; thus helping to identify them, to classify them using the anatomical characters. It had been found that all the species have barrel-shaped epidermis of one layer. Hairs were found in two groups:basal cells in one row with smooth wall which include (H. bacciferum and H. supinum) ,basal cells in many rows and the wall is glandular (H. ovalifolium,H. strigosum and H. sudanicum). The hypodermis consist of collenchymatous cells except H. bacciferum which have paranchymatous cells cells. Whereas the general cortex composed of paranchymatous cells. Pholem element and xylem are noted. The transverse sections of the leaves showed that the mesophyle consist of 2-5 layers of spongi cells, palisade layers varied from (1–4) layers, the main vascular bundle was one in all studied species, lateral bundles was absent in H. ovalifolium and it differs from 2 in (H.strigosum ,H. bacciferum and H. supinum) to 4 in (H. sudanicum). The stomata length and width were measured, moreover stomata indices were calculated and it was found to be similar within the genus Heliotropium.