Pycnandra Benth., a member of subfamily Chrysophylloideae (Sapotaceae), is the largest endemic genus in New Caledonia and is subdivided into six subgenera. It circumscribes 59 species, plus an additional three described here, and nine additional species that remain undescribed for various reasons. We here use nrDNA data of ETS, ITS, and RPB2, analyse it within a Bayesian framework using BEAST, and place the new species in their respective subgenera. Pycnandra perplexa Swenson & Gâteblé is placed in subgenus Achradotypus and given a preliminary IUCN Red List assessment of Near Threatened (NT). It is confined to the ultramafic massif of southern Grande Terre and separated from the similar species P. griseosepala Vink, which is confined to non-ultramafic mountains north of the large southern ultramafic plateau. Pycnandra kopetoensis Munzinger & Swenson and P. margueriteae Munzinger & Swenson are two new micro-endemic species known only from their type localities, where habitats have been destroyed by deforestation, deliberate fires and mining activities. Pycnandra kopetoensis is named after Mount Kopéto, placed in subgenus Leptostylis, and given a preliminary assessment as Critically Endangered (CR). Pycnandra margueriteae is from a small remnant forest near Bourail and categorised as Critically Endangered (CR). Revised identification keys for subgenus Achradotypus, Leptostylis and Pycnandra are provided.