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Chlorophyllum accommodates lamellate agaricoid species as well as sequestrate angiocarpic taxa, which do not form a monophyletic lineage within the genus. To clarify phylogenetic affinities and delimit species boundaries among sequestrate representatives of the genus, we analyzed historical and contemporary material from a broad geographic range, encompassing North America, southern Africa, eastern Asia, the Greek and Iberian peninsulas, and the Mediterranean islands of Cyprus and Lesvos. Six sequestrate lineages of Chlorophyllum were identified, which appear to have evolved in at least three independent gasteromycetation events. Multigene analysis of the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of the nuc 28S rDNA (28S), RNA polymerase II second largest subunit ( rpb2 ), and translation elongation factor 1-α ( tef1 ) genes revealed the presence of a previously undescribed species, introduced here as Chlorophyllum levantinum , sp. nov. Its sister species C. lusitanicum , previously known only from Spain, is shown to have a wider distribution throughout the Mediterranean basin. A South African collection of Secotium gueinzii , a poorly known taxon described in 1840 and seldom appearing in literature since, was also shown to nest within Chlorophyllum . An epitype for this rare species is designated, Secotium becomes a priority synonym of Chlorophyllum , and nomenclatural implications are discussed. The phylogenetic placement of C. arizonicum is confirmed after successful sequencing of the century-old holotype and an undescribed sister lineage of this species detected. Emended descriptions of sections Chlorophyllum, Endoptychorum , and Sphaerospororum are provided to reflect current results, along with updated descriptions and extensive imagery for all known sequestrate taxa of Chlorophyllum .