About one hundred years ago, Dykes noticed an innovative feature in Iris, a raised central ridge along the midvein of the sepal, that he called a crest. Molecular phylogenetic and ancestral state reconstruction studies suggested that the sepal crest is a homoplastic character, even though the majority of the crested species form a monophyletic group. We investigated the putative multiple origins of sepal crests in Iris and relationships among crested species via comprehensive sampling of crested species in Iris using five plastid markers. We employed maximum parsimony, maximum likelihood, and Bayesian inference in reconstructing relationships. Our data analyses resolved a large core-crested clade along with four other independent lineages that also have crested species. Within the core-crested clade, four highly supported major clades were identified comprising species from subgen. Nepalensis and Scorpiris and some species from subgenus Limniris section Lophiris sensu Mathew. However, relationships among these four major clades were not fully resolved. Six species from section Lophiris represent four additional origins of the sepal crest.