In mouse fetal gonads, sex differentiation begins at 10.5–11.5 days postcoitum (dpc). With XY gonads of 12.5 dpc, cord-like structures are visible and stromal cells migrate from adjacent mesonephros, unlike in XX gonads. However, the migrated mesonephric cells, except for the endothelial cells, have not been specifically identified because they have not expressed differentiation markers over the course of organ coculture in previous experiments. In this study, we have for the first time succeeded in isolating only the mesonephric cells that migrate into the XY gonad from the mesonephros with alive and then cultured these cells in vitro through the use of an organ coculture system using EGFP-transgenic mice and a FACS Vantage. The migrated and isolated cells were used for morphological and molecular characterization. The migrated mesonephric cells contained three cell forms; a sharp cell form, a round cell form, and a cluster-forming cell. The sharp cells have the characters of peritubular myoid cells. The round cells and cluster-forming cells have the potential to differentiate into Leydig cells, as some of them are 3β-HSD-positive. In in vitro culture of migrated mesonephric cells, the cluster-forming cells proliferated well and then differentiated into round cells, suggesting that the cluster-forming cells may be stem or precursor cells for the round cells. Thus, our findings provide important information related to the migration and differentiation of migrated mesonephric cells in the XY gonad.