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Abstract Human mesenchymal stem cells (hMSCs) have gained traction in transplantation therapy due to their immunomodulatory, paracrine, immune‐evasive, and multipotent differentiation potential. The inherent heterogeneity of hMSCs poses a challenge for therapeutic treatments and necessitates the identification of robust biomarkers to ensure reproducibility in both in vivo and in vitro experiments. In this study, we utilized dielectrophoresis (DEP), a label‐free electrokinetic phenomenon, to investigate the heterogeneity of hMSCs derived from bone marrow (BM) and adipose tissue (AD). The electrical properties of BM‐hMSCs were compared to homogeneous mouse fibroblasts (NIH‐3T3), human fibroblasts (WS1), and human embryonic kidney cells (HEK‐293). The DEP profile of BM‐hMSCs differed most from HEK‐293 cells. We compared the DEP profiles of BM‐hMSCs and AD‐hMSCs and found that they have similar membrane capacitances, differing cytoplasm conductivity, and transient slopes. Inducing both populations to differentiate into adipocyte and osteoblast cells revealed that they behave differently in response to differentiation‐inducing cytokines. Histology and reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) analyses of the differentiation‐related genes revealed differences in heterogeneity between BM‐hMSCs and AD‐hMSCs. The differentiation profiles correlate well with the DEP profiles developed and indicate differences in the heterogeneity of BM‐hMSCs and AD‐hMSCs. Our results demonstrate that using DEP, membrane capacitance, cytoplasm conductivity, and transient slope can uniquely characterize the inherent heterogeneity of hMSCs to guide robust and reproducible stem cell transplantation therapies.