Chondromyxoid fibroma is an uncommon benign cartilaginous tumor that rarely presents in the sino-nasal region as a locally destructive, erosive lesion. Both clinically and histologically, it is a difficult diagnosis and can be confused with malignant processes such as myxoid chondrosarcoma. Histology of the tumor, especially with a small sample, can be challenging because of its heterogeneous nature showing an admixture of fibrous, myxoid, and chondroid areas. We are reporting unique cytogenetic findings in a case of chondromyxoid fibroma involving the floor of the nasal cavity with a clonal rearrangement between chromosomes 6 and 19. To our knowledge, karyotypes of 14 cases are reported in literature, with 11 cases reporting nonrandom, clonal abnormalities of chromosome 6. These results illustrate the distinctive nature of this tumor and may help identify genes involved in the pathogenesis of this tumor.