The Oceanian plant genus Spiraeanthemum (Cunoniaceae) has a centre of diversity in New Caledonia, where it is represented by seven species. Its diversification was investigated using two low-copy nuclear genes, ncpGS and GapC, and phylogenetic analyses were based on maximum parsimony, maximum likelihood and recombination networks. We detected several cases of gene recombination in both datasets, and these have obscured the history within the genus. For S. ellipticum and S. pubescens, accessions from southern populations on ultramafic soils were genetically distinct from accessions from northern populations on non-ultramafic soils. Given that no obvious morphological characters distinguish northern and southern populations in either taxon, both may be considered as examples of cryptic species. Incongruence between gene trees and species' delimitation may be explained by the parallel evolution of similar morphology, differential lineage sorting leading to differential fixation of alleles or different introgression patterns in the north and south leading to allele displacement. In New Caledonia, some species with broad ecological preferences may thus be artificial concepts. This suggests that they should be treated more critically in monographs and that the species' richness of the New Caledonian flora may be underestimated. Problems associated with the typification of S. ellipticum and evidence of hybridization events in the history of Spiraeanthemum are also discussed.