Chondrosarcoma is the second most common primary malignant bone tumor and is resistant to chemotherapy and radiation. Inadequate treatment response and poor prognosis requires novel therapeutic approaches. Proline‑rich polypeptide‑1 (PRP‑1), synthesized by brain neurosecretory cells, has demonstrated antitumor properties in JJ012‑cells; however, its underlying molecular mechanism remains unclear. The present study aimed to investigate the epigenetic regulation by which PRP‑1 inhibits chondrosarcoma cancer stem cell (CSC) proliferation and to elucidate additional CSC biomarkers in human chondrosarcoma other than ALDH1A1. Human chondrosarcoma JJ012‑cells were treated with PRP‑1 prior to performing an Aldefluor™ assay and fluorescence‑activated cell sorting in order to determine aldehyde dehydrogenase (ALDH) expression levels and isolate ALDHhigh and ALDHlow cell populations. ALDH is an established marker of CSCs in several neoplasms, including chondrosarcoma. The cells were collected and lysed for gel electrophoresis, followed by western blot analysis. The Aldefluor™ assay was used to assess the expression levels of well‑established CSC biomarkers, including CD133, CD4, CD10, CD144, CD177, CD221, CD271, leucine‑rich repeat‑containing G protein‑coupled receptor 5, SOX2 and B lymphoma Mo‑MLV insertion region 1 homolog (BMI‑1), within the ALDHhigh population of JJ012 cells. The results confirmed that ALDHA1 was the biomarker for chondrosarcoma CSCs. PRP‑1 was demonstrated to inhibit the ALDHhigh population colony and sarcosphere formation; 5 µg/ml PRP‑1 was indicated to be the optimum concentration in eliminating colonies formed by JJ012 cells (92%, P<0.001) and by the ALDHhigh CSC‑population (80.5%, P<0.001) in the clonogenic dose‑response assay. Spheroid growth unequivocally decreased with an increase in PRP‑1 dose. In order to determine the molecular mechanism by which PRP‑1 decreased the CSC population, the regulation of the mammalian Switch/sucrose non‑fermenting (SWI/SNF) complex, also referred to as BRG1‑associated factor (BAF) complex, which either activates or represses transcription, thus acting as an oncogene or tumor suppressor in human cells, was analyzed. PRP‑1 was demonstrated to decrease the expression levels of BRG, BAF170 and BRM; therefore, in JJ012 cells, these key players of the SWI/SNF (BAF) complex served an oncogenic role. The results of the present study demonstrated that PRP‑1 targets chromatin‑remodeling complexes; therefore, future efforts will be directed towards determining the interconnection between CSC maintenance, self‑renewal capacity and BAF complexes.Keywords: chondrosarcoma; cancer stem cells; aldehyde dehydrogenase; proline-rich polypeptide-1.