Background Mucosal melanoma is the second most common subtype of melanoma in China and head and neck region is one of the main sites of this disease. Aims/Objectives Analyzed the phenotypes of C-Kit, NRAS, PDGFRA and BRAF genes in patients with in different locations to explore the characteristics of gene mutations. Material and Methods 96 patients were included in this study. C-Kit (exons 9, 11, 13, 17 and 18), NRAS (exons 1 and 2), PDGFRA (exons 12, 14 and 18) and BRAF (exons 11 and 15) were analyzed by PCR amplification and Sanger sequencing. Results 14 (14.58%) patients had C-Kit mutation, 6 (6.25%) had BRAF mutation, 23 (23.96%) had PDGFRA mutation, and 12 (12.50%) had NRAS mutation. The NRAS mutation (p = 0.037, 95%CI: 1.050-4.572) was an independent factor affecting distant metastasis and was most commonly found in the nasal cavity/paranasal sinuses (p = .043) while the BRAF mutation was more common in locations other than the nasal cavity/paranasal sinus (p = .008) and was associated with local recurrence. Conclusions and Significance Gene phenotypes of mucosal melanoma in different locations has differences. Lesions in the nasal cavity and paranasal sinus should be assessed separately from other parts such as the nasopharynx.