Background and Objective: Mesenchymal stem cells are promising sources of stem cells for tissue repair because of their ability to differentiate into different cells, easy proliferation and culture, and immunomodulatory properties. Despite extensive research on the immunophenotype of mesenchymal stem cells, a lack of specific markers comprises challenges for researchers. The aim of this research was to isolate and expand murine lung and adipose derived mesenchymal stem cells and to compare their expression of surface protein markers. Materials and Methods: Mesenchymal stem cells were isolated from murine lung and adipose tissues. Specific differentiation media were added for differential investigations. Finally, the expression of surface antigens were measured by flow cytometry and compared in both cell populations. Results: Mesenchymal stem cells from both tissues were proliferated well and adipocyte and osteocyte differentiations were observed. Moreover, they showed CD73, CD105 and CD90 expression, but no expression of CD34, CD45 and CD11b was observed. In this study, lung CD105+ mesenchymal stem cells possessed lower percentage than those in adipose tissue. Conclusion: Mesenchymal stem cells were isolated from lung similar to adipose derived mesenchymal stem cells and expressed common markers associated with adipose tissue mesenchymal stem cells.