The role of somatic protein-coding mutations in the development of cancer is well established. However, it is less clear whether non-coding mutations in cis-regulatory regions also contribute to cancer development. Following the recent discovery of recurrent mutations in the TERT promoter in melanoma1, identification of other cis-regulatory somatic mutations in cancers is of considerable interest. In this study, we used publically available somatic mutation calls in the whole genome sequenced (WGS) COLO-829 metastatic malignant melanoma cell line2, along with matched genome-wide chromatin accessibility and histone modification data from normal melanocytes, to identify mutations within cis-regulatory elements. In total, 23 potential promoter mutations were identified. The functional consequence of these mutations was then assessed using reporter assays. Of 23 promoter regions tested, four mutations were identified which altered promoter activity relative to wild-type sequences. One such mutation lies within the promoter region of NDUFB9, a gene involved in oxidative phosphorylation, and potentially associated with melanoma3 and metastasis4. Bioinformatics analysis indicates that this mutated base is highly conserved and potentially disrupts a Krüppel-like factor binding motif which may explain the decrease in NDUFB9 promoter activity. To further evaluate these mutations in metastatic melanomas, somatic mutations were called in a cohort of 34 WGS cutaneous melanoma samples from The Cancer Genome Atlas (TCGA). We observed particularly high rates of recurrence among promoter mutations, including mutations in the NDUFB9 promoter which are present in ~ 5% of this cohort. Taken together, we have established a general methodology to identify and validate potential cis-regulatory driver mutations from cancer WGS datasets, and identified a potential driver mutation in the promoter of NDUFB9 in metastatic melanoma.