Despite recent advances in molecular phylogenetic studies, deep evolutionary relationships in Cyperaceae are still not entirely resolved. Reduction of floral morphology and complex inflorescences pose difficulties to unravel relationships based on morphology alone. One of the most phylogenetically informative structures in Cyperaceae are the embryos. The utility of embryo characters and types in Cyperaceae systematics is reviewed in a molecular phylogenetic context using a DNA supermatrix incorporating sequences from five plastid (matK, ndhF, rbcL, rps16, trnL-F) and two nuclear ribosomal (ETS, ITS) regions. The phylogenetic hypothesis presented includes the most extensive sampling of the family to date. Fourteen qualitative morphological embryo characters were coded, ancestral state reconstructions were performed, and the embryo of each sampled genus was classified in a typological system based on key morphological features. Embryo morphology provides a valuable source of independent data for Cyperaceae systematics that can be used to place species with unknown affinities, when molecular data is not available, or when results of analyses are inconclusive or conflicting. Integrating embryo data will remain critical for future higher level studies of Cyperaceae evolution and classification.