Background: In Australia, melanoma remains one of the most deadly cancers, where the estimated risk of being diagnosed by the age of 85 is one in 18. Melanoma risk phenotypes, such as red hair and fair skin, have been well established. This study correlated phenotypic data, such as skin reflectance, freckling, naevus patterns, and genotypic information with the development of skin cancer. Objectives: To examine the relationships between counts of naevi of each dermoscopic pattern (globular, reticular, nonspecific), and signature naevus pattern with Fitzpatrick Skin Type and constitutive skin colour. We aimed to correlate skin colour, hair colour, naevus counts and degrees of freckling with genotypic findings; including MC1R, IRF4, TYR and TPCN2 genotypes. Sun protective habits were also examined, particularly in relation to age. Design: Constitutive skin colour was measured objectively using a spectrophotometer, and a device that can take both a body overview and dermoscopic sequential images of naevi. Skin types and freckling scores were determined by examination of total body images. Genetic data was obtained from saliva samples provided by participants. Data analysis was undertaken using non-parametric tests for association. Participants: Participants were defined as melanoma “cases”, high-risk individuals (with a history of melanoma in a first-degree relative), and “controls” with no history of melanoma. A further set of controls was also recruited from the Brisbane Longitudinal Twin Study. A total of 1845 individuals participated in the study. Results: Significant differences were demonstrated between constitutive skin colour and signature naevus pattern per individual (Kruskal-Wallis test p = 0.007). Higher freckling scores were significantly more likely to be associated with lighter skin colour and a nonspecific or reticular naevus pattern and an MC1R RHC variant genotype (p = 5.37 x 10-12). TPCN2 SNPs rs3750965, rs2376558 and rs10896418 demonstrated the significant influences over hair colour, whilst rs2376558, rs4930263 were strongly associated with skin colour. Conclusions: Different categories of skin colour exhibit differences in dermoscopic naevus pattern counts and signature naevus patterns. An influence of genes associated with melanoma risk phenotypes, such as MC1R, was also observed. The rs12203592 SNP of IRF4 was associated with pale skin and freckling. We also observed synergistic genetic interactions between MC1R, IRF4 and TYR. These findings may aid melanoma risk stratification and clarify the influence of genetics on phenotype.