A squamous-cell carcinoma (SCC) of the lung can be indistinguishable from metastatic SCC of gynecologic origin using common histopathologic techniques; however, establishing tumor origin can be clinically relevant. A patient with a Bartholin gland SCC was found to also have a pulmonary SCC, concerning for metastasis versus synchronous pulmonary primary. Hematoxylin and eosin and immunohistochemistry alone could not differentiate the lesion, and both tumors were human papilloma virus positive. Allelotyping for loss of heterozygosity established the pulmonary lesion as a rare event of vulvar pulmonary metastasis. The patient received palliative chemotherapy instead of curative treatment. Allelotyping for loss of heterozygosity is an effective tool to establish metastasis versus synchronous primary tumors in the presence of multiple lesions, helping to direct appropriate clinical management.