Display omitted •Analyses showed resolution among 1/3 of the Diospyros species form NC clade III.•Some morphological distinct species could not be discriminated with the markers used.•Diospyros arrived relative recently (5–20mya) in New Caledonia.•Chromosome counts confirmed the investigated species to be diploid.•Genome sizes varied nearly fourfold among species examined. To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK–matK and trnS–trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around 9million years ago. The oldest species are around 7million years old and the youngest ones probably much less than 1million years.