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Understanding how genetic variation is spatially distributed is necessary for understanding the processes that generate and maintain biodiversity. However, there has been little investigation into the phylogeography of widespread forest trees in Aotearoa New Zealand with studies to date showing little congruence in phylogeographic patterns. Pseudopanax crassifolius (lancewood/horoeka) is a widespread lowland forest tree endemic to Aotearoa New Zealand. We investigated the phylogeography of this species using microsatellites and chloroplast haplotypes and compare the results to published results from the closely-related P. ferox, which also has a widespread lowland distribution, but differs in its ecological preferences. Microsatellite genotypes revealed two weakly differentiated genetic clusters within P. crassifolius. One cluster comprised all individuals from the North Island plus those from the north-eastern and central-eastern South Island. The second cluster, which had lower levels of genetic variation than the northern cluster, encompassed the southern and western South Island. The southern cluster exhibited lower genetic diversity, particularly in the southern South Island, suggesting that the species was severely restricted, or even extirpated, from this region during the Last Glacial Maximum (LGM). This result contrasts with the high level of genetic structuring observed in the closely-related P. ferox. There was evidence of asymmetric chloroplast introgression from P. ferox into P. crassifolius in the south-eastern South Island. Alternative scenarios that may have led to this asymmetric introgression are discussed.