The seed morphology of nine taxa of Juncus from Egypt has been investigated using light and scanning electron microscopy, to determine the importance of seed coat features as taxonomic characters. Macro- and micromorphological characters, including seed shape, color, size, seed appendages, epidermal cell shape, anticlinal boundaries, and outer periclinal cell wall and secondary cell wall sculpture are presented. Four types of seed appendages are recognized: (i) seeds with two appendages; (ii) seeds without appendages; (iii) seeds with minutely a piculate at one end; and (iv) seeds with minutely a piculate at both ends. Two types of anticlinal cell wall boundaries,(i) raised-channeled, straight and (ii) raised, straight or sinuous, and three different shapes of outer periclinal cell wall are described: (i) flat; (ii) concave; and (iii) flat to slightly concave. The secondary sculpture of the cell wall varies from striate to microreticulate or reticulate, and smooth to finely folded. Seed characters provide useful data for formulating the taxonomy of Juncus both on the subgeneric and sectional level. A key for the identification of the investigated taxa based on seed characters is provided.