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Introduction Forensic anthropologists routinely apply metric and non-metric methods to aid in ancestry estimation of unknown skeletal remains. Within the South African (SA) context, legislation implemented during the 20th century may have affected the genetic makeup of population groups to such an extent that differentiation of ancestral groups is a distinct possibility. This study aimed to assess whether trait analysis of the nasal region, using metric and non-metric methods, is an effective approach to differentiation between the three dominant (coloured, black, and white) SA population groups, which is of importance for forensic purposes. Methods Analysis was conducted on crania (n = 196) of known sex, age at death and ancestry. Crania were obtained from two osteological collections in SA. Metric traits measured include the interorbital breadth, nasal height and interaperture width, while the non-metric traits include the extent of the anterior nasal spine, the nasal bone contour, inferior nasal aperture, nasal aperture shape and nasal overgrowth. Results Results showed that four of the five non-metric traits yielded statistically significant differences between the three examined groups. For the three metric traits, significant differences were found between all groups for all traits assessed. Discussion The SA coloured population showed the most intra-population variation and was more closely related to the SA black group with regards to the non-metric traits. The white population group had limited intra-population variation, which provides a basis for differentiating this group from the other groups assessed. In conclusion, differentiation of these three groups is possible, despite the extent of overlapping population variation, when all traits are looked at in combination rather than conducting individual trait analysis.