Long non‑coding RNAs (lncRNAs) serve a critical role in various biological processes including cell growth, transcriptional regulation and differentiation. Previous studies have demonstrated that human amnion‑derived mesenchymal stem cells (HAMSCs) possess the potential to promote proliferation and osteogenic differentiation of human bone marrow mesenchymal stem cells (HBMSCs). However, little is known about the roles of lncRNAs in these mechanisms. The present study investigated the expression of lncRNAs in HBMSCs co‑cultured with HAMSCs to study their involvement in the mechanism of osteogenic differentiation. RNA sequencing was used to compare the lncRNA expression profiles of HBMSCs co‑cultured with or without HAMSCs during osteogenic differentiation. A total of 339 differentially expressed lncRNAs were identified [log2 (fold change)>2.0 or <‑2.0; P<0.05], consisting of 131 downregulated and 208 upregulated lncRNAs. Among these lncRNAs, it was identified that the lncRNA‑differentiation antagonizing non‑protein coding RNA (DANCR) expression level in HBMSCs was significantly decreased by co‑culturing with HAMSCs, and DANCR overexpression inhibited the effect of HAMSCs on the promotion of runt‑related transcription factor 2 expression. These data suggested that HAMSCs are likely to regulate differentiation processes in HBMSCs by influencing the DANCR, thus offering a novel insight into the complicated regulation mechanisms of HAMSC‑derived osteogenic differentiation.