Objective To explore the feasibility of labeling and tracing in vitro goat bone marrow mesenchymal stem cells (BMSCs) by bromodeoxyuridine (BrdU) on the basis of investigation of its optimal concentration, incubating time and cytotoxicity. Methods A healthy goat, aged 10 months old, male, weighing 32 kg, was used in this study. Bone marrow was aspirated. BMSCs were isolated and cultured using the adherence method in vitro. The fourth passage of BMSCs (P4) were incubated with BrdU at 5, 10, 15, 20 μmol/L as 5, 10, 15, 20 μmol/L BMSC groups. Cells were not labeled by BrdU as negative control. The following parameters were measured: induction, differentiation and determination of goat BMSCs; the optimal mass concentration and incubation time of 5-BrdU labeling; cell positive rate at 12, 24, 48 and 72 hours in each group using immunofluoreseenee; the cell survival rate after various concentrations of BrdU ladling by trypan-blue exclusion. Results The morphology of the primary and passage goat BMSCs was fusiform in shape. Goat BMSCs could differentiate into osteoblasts and chondrocytes following induction. BMSC nucleus showed green fluorescence under fluorescence microscope after being labeled by BrdU. The mean labeling rate increased with the increase in the concentration and incubation time of BrdU, and reached to (93.32± 3.25)% after incubation in 15 μmol/L, BrdU for 48 hours. There were no significant differences between 15 μmol/L BrdU for 72 hours, 20 μmol/L BrdU for 48 hours and 72 hours (P > 0.05), or between the other groups or time points (P < 0.05). The labeling rate of the blank control group was 0. The cell survival rate was all above 90% (P > 0.05). Conclusions BrdU can be used as a labeling marker for goat BMSCs. When the concentration is 15 μmol/L and the incubation time is 48 hours, the optimal labeling effect can be achieved. Goat BMSCs labeled with BrdU is of high efficiency and safety.