High naevus count is the strongest risk factor for melanoma and although gene variants have been discovered for both traits, epigenetic variation is unexplored. We investigated 322 healthy human skin DNA methylomes associated with total body naevi count, incorporating genetic and transcriptomic variation. DNA methylation changes were identified at genes involved in melanocyte biology, such as RAF1 (p = 1.2 x 10(-6)) and CTC1 (region: p = 6.3 x 10(-4)), and other genes including ARRDC1 (p = 3.1 x 10(-7)). A subset exhibited coordinated methylation and transcription changes within the same biopsy. The total analysis was also enriched for melanoma-associated DNA methylation variation (p = 6.33 x 10(-6)). Additionally, we show that skin DNA methylation is associated in cis with known GWAS SNPs for naevus count, at PLA2G6 (p = 1.7 x 10(-49)) and NID1 (p = 6.4 x 10(-14)), as well as melanoma risk, including in or near MC1R, MX2 and TERT/CLPTM1L (p < 1 x 10(-10)). Our analysis using a uniquely large dataset comprising healthy skin DNA methylomes identified known and additional regulatory loci and pathways in naevi and melanoma biology. This integrative study improves our understanding of predisposition to naevi and their potential contribution to melanoma pathogenesis.