Visualization of differentiating germ cells is critical to understanding the formation of primordial follicles in the ovary, and the commitment of spermatogonial stem cells to differentiation. We engineered and generated a BAC transgenic mouse line, Sohlh1-mCherryFlag (S1CF), under the direction of the native Sohlh1 promoter. Sohlh1 is a germ cell-specific gene that encodes the basic helix-loop-helix (bHLH) transcriptional regulator that is essential in oogenesis and spermatogenesis. Sohlh1 expression is unique, and is limited to perinatal and early follicle oocytes and differentiating spermatogonia. The Sohlh1-mCherryFlag transgene was engineered to fuse SOHLH1 to the red fluorescent protein CHERRY with 3-tandem-FLAG tags. S1CF animals fluoresce specifically in the oocytes of perinatal ovaries and small follicles in adult ovaries, as well as in spermatogonia, a pattern that is similar to endogenous SOHLH1. Moreover, S1CF rescued germ cell loss and infertility in both male and female Sohlh1(-/-) animals. The FLAG-tag on S1CF was effective for immunostaining and immunoprecipitation. The Sohlh1-mCherryFlag transgenic mouse provides a unique model to study early germ cell differentiation, as well as in vivo imaging and purification of differentiating germ cells.