Objective Cancer stem cells (CSC) comprise a subpopulation of tumor cells associated with initiation, progression, and chemoresistance. Subpopulations of CSC were characterized in a metastatic cell line LN1-A derived from the oral squamous cell carcinoma (OSCC), previously isolated in our laboratory. Study Design We selected three subpopulations of CSC (CD44Low/CD326+, CD44+/CD326-, and CD44High/CD326-) among the seven phenotypes isolated by labeling CD44 and CD326 antibodies by flow cytometry in metastatic LN-1A cells. Cell morphology, proliferation, migration, adhesion, clonogenic assay, cell cycle, cell death, and cisplatin chemoresistance were characterized. Western blotting for EFGR, FASN, p-AKT, CPT1-α, and mesenchymal epithelium transition markers were performed. Results CD44Low/CD326+ subpopulations showed an epithelial phenotype with polygonal morphology and high E-cadherin expression, while CD44+/CD326- and CD44High/CD326- showed fusiform morphology with high Vimentin and Slug expressions, suggesting a mesenchymal phenotype. Proliferation was higher in CD44+/CD326- and CD44High/CD326- cells, which was accompanied by increased levels of p-AKT. Cell adhesion and colony formation were increased in CD44+/CD326- and CD44High/CD326-, while cell death was higher in CD44Low/CD326+. No significant differences in cell cycle, cisplatin resistance, and the expression of EGFR, FASN, and, CPT1-α were observed between phenotypes. Conclusion Our results showed that CD44+/CD326- and CD44High/CD326- cells show a more aggressive phenotype. Cancer stem cells (CSC) comprise a subpopulation of tumor cells associated with initiation, progression, and chemoresistance. Subpopulations of CSC were characterized in a metastatic cell line LN1-A derived from the oral squamous cell carcinoma (OSCC), previously isolated in our laboratory. We selected three subpopulations of CSC (CD44Low/CD326+, CD44+/CD326-, and CD44High/CD326-) among the seven phenotypes isolated by labeling CD44 and CD326 antibodies by flow cytometry in metastatic LN-1A cells. Cell morphology, proliferation, migration, adhesion, clonogenic assay, cell cycle, cell death, and cisplatin chemoresistance were characterized. Western blotting for EFGR, FASN, p-AKT, CPT1-α, and mesenchymal epithelium transition markers were performed. CD44Low/CD326+ subpopulations showed an epithelial phenotype with polygonal morphology and high E-cadherin expression, while CD44+/CD326- and CD44High/CD326- showed fusiform morphology with high Vimentin and Slug expressions, suggesting a mesenchymal phenotype. Proliferation was higher in CD44+/CD326- and CD44High/CD326- cells, which was accompanied by increased levels of p-AKT. Cell adhesion and colony formation were increased in CD44+/CD326- and CD44High/CD326-, while cell death was higher in CD44Low/CD326+. No significant differences in cell cycle, cisplatin resistance, and the expression of EGFR, FASN, and, CPT1-α were observed between phenotypes. Our results showed that CD44+/CD326- and CD44High/CD326- cells show a more aggressive phenotype.