Melanoma aetiology has been proposed to have two pathways - determined by naevi and type of sun exposure - and related to the anatomical site where melanoma develops.We examined associations with melanoma by anatomical site for a comprehensive set of risk factors including pigmentary and naevus phenotypes, ultraviolet radiation exposure, and polygenic risk.We analysed harmonised data from 2,617 people with incident first invasive melanoma and 975 healthy controls recruited through two population-based case-control studies in Australia and the United Kingdom. Questionnaire data were collected by interview using a single protocol, and pathway-specific polygenic risk scores were derived from DNA samples. We estimated adjusted odds ratios (ORs) using unconditional logistic regression that compared melanoma cases at each anatomical site with all controls.Comparing case with control participants, there were stronger associations for many versus no naevi for melanomas on the trunk, upper and lower limbs than on the head and neck (P-heterogeneity <0.001). Very fair skin (vs. olive/brown skin) was more weakly related to melanoma on the trunk than to melanomas at other sites (P-heterogeneity=0.04). There was no significant difference by anatomical site for polygenic risk. Increased weekday sun exposure was positively associated with melanoma on the head and neck but not on other sites.We found evidence of aetiological heterogeneity for melanoma, supporting the dual pathway hypothesis. These findings enhance understanding of risk factors for melanoma and can guide prevention and skin examination education and practices.