The Marquesas Islands have traditionally been divided into a northwestern and a southeastern group, a division which reflects language dialect differences. Additionally, archaeological studies have also suggested that differences in material culture existed between the northwestern and southeastern islands. This study examines Marquesan cranial discrete and metric traits to evaluate the level of intra-archipelago heterogeneity, and to determine if a northwest/southeast division is evident cranially. The data consist of 28 cranial discrete traits and 49 craniofacial measurements of prehistoric Marquesans. Male and female data are pooled for discrete trait and metric data, following a Z-score standardization technique adjustment. The data represent three island samples: Nuku Hiva (northwest), Fatuiva (southeast), and a combined Tahuata/Hiva 'Oa (southeast). Of the 28 discrete traits, 16 are utilized in a mean measure of divergence analysis that provides scores of 0.259 for Fatuiva-Tahuata/Hiva 'Oa, 1.850 for Nuku Hiva-Fatuiva, and 1.491 for Nuku Hiva-Tahuata/Hiva 'Oa. Of the 49 craniofacial measurements, 46 are utilized in RMET/NORM analyses, providing unbiased D(2) values of 0.0433 for Fatuiva-Tahuata/Hiva 'Oa, 0.1328 for Nuku Hiva-Fatuiva, and 0.0813 for Nuku Hiva-Tahuata/Hiva 'Oa. The islands of the southeastern group are closer to each other than either was to the island of the northwestern group. When a sample from 'Ua Huka is included in the craniometric analysis, the unbiased D(2) values of 0.0829, 0.1175, and 0.0431 are calculated for 'Ua Huka and Nuku Hiva, and Fatuiva and Tahuata/Hiva 'Oa pairings, respectively, indicating a close similarity of 'Ua Huka to the southeastern islands. Mean measure of divergence analysis of cranial discrete traits as well as RMET/NORM analyses of craniometric variables reveal that differences exist between the islands of the northwestern and southeastern Marquesas Islands. These results support previous research that documented linguistic and cultural differences between these regions of the archipelago. However, the results indicate that 'Ua Huka, an island traditionally included in the northwestern Marquesas Islands, has an affinity to the southeastern Marquesas Islands, possibly due to its pivotal position as a waypoint in the Marquesas Island interaction sphere.