We analysed nine microsatellite markers for 626 individuals representing the geographic range of eight closely related endemic New Zealand species of Sophora. Structure analysis identified the optimal K value as seven, with samples identified as Sophora chathamica, Sophora fulvida, Sophora longicarinata, and Sophora prostrata retrieved as well-defined groups. The remaining samples formed less resolved groups referable to Sophora tetraptera and Sophora godleyi, with Sophora microphylla and Sophora molloyi forming the seventh group. Our data suggest that considerable admixture occurs and this is most likely the result of hybridisation or introgression. S. fulvida shows admixture with the sympatric S. chathamica, and the widespread S. microphylla exhibits admixture with the sympatric S. godleyi, S. molloyi, and S. tetraptera.