<p>Craniofacial morphometrics provide valuable insights into population-specific variations, aiding ethnic affiliation estimation in forensic anthropology and clinical reconstructive applications. Nigeria’s ethnic diversity, with over 250 groups, shows distinct facial and nasal patterns, but data on minority groups like the Afemai (Edo North) remain limited. This cross-sectional study examined morphometric variations among Afemai students to assess sub-ethnic differences and potential for ethnic identification. A total of 150 Afemai students (aged 16–30 years) at Ambrose Alli University, Ekpoma, were recruited via random sampling after screening 330 individuals (210 excluded). Direct anthropometric measurements (facial height/breadth, nasal height/width, interpupillary distance, nasolabial angle) were taken using digital callipers and tape, with indices calculated (facial index; nasal index). Parameters were stratified by sub-ethnic ancestry area (six local government areas), gender, and parental ethnic homogeneity. Data were analysed using one-way ANOVA and independent t-tests, with significance at <i>p</i> ≤ 0.05. The sample was 80% male (<i>n</i> = 120) and 20% female (<i>n</i> = 30). Predominant phenotypes were hyperleptoprosopic faces (54%) and hyperplatyrrhine noses (62%). ANOVA showed significant ancestry-area differences in nasal width (<i>p</i> &lt; 0.001), nasal height (<i>p</i> = 0.037), nasolabial angle (<i>p</i> = 0.020), facial height (<i>p</i> &lt; 0.001), and facial breadth (<i>p</i> &lt; 0.001). Gender differences were significant for nasal height, nasolabial angle, facial height, and interpupillary distance (all <i>p</i> &lt; 0.001). Parental descent affected only nasal height (<i>p</i> = 0.013). Sub-ethnic and gender variations in craniofacial parameters support their utility for ethnic affiliation estimation within Afemai, providing normative data for forensic and clinical use in Nigeria. Balanced gender sampling and advanced techniques are recommended for future studies.</p>