The order Caryophyllales comprises 26 families distributed all over the world. In Pakistan it is represented by 14 families viz., Aizoaceae, Amaranthaceae, Basellaceae, Cactaceae, Caryophyllaceae, Frankeniaceae, Gisekiaceae, Molluginaceae, Nyctaginaceae, Phytolaccaceae, Plumbaginaceae, Polygonaceae, Portulacaceae and Tamaricaceae. Detailed macro and micro morphological characters of seeds of 229 taxa belonging to the order Caryophyllales were examined by using light and scanning electron microscopy including seed descriptions, keys and micrographs. Considerable variation was observed in seed size, shape, colour and surface at family, generic, specific or infraspecific levels. The comprehensive study on seed morphology is first of its kind and provides an additional tool to strengthen the recognition of taxa within the order caryophyllales from Pakistan. This data is further analysed numerically by clustering to trace out the phylogenetic relationship of taxa at various levels.