Identification of specific marker proteins in cells is useful for isolating cells and determining their cellular characteristics and functions. Based on our previous study showing that matrix metalloproteinase 9 (MMP-9) can be used as a marker for porcine spermatogonia, the expression pattern of MMP-9 was determined in both pre- (5-month old) and post-pubertal (11–month old) bovine testes. Histological analysis revealed that spermatogonia were located near the basement membrane in both testes, while spermatozoa were not detected in the 5-month old pre-pubertal bovine testes and epididymides. Mature spermatozoa were observed in the 11-month bovine testes and epididymides, and MMP-9 expression in 11-month old bovine testes was lower than 5-month old testes, according to reverse transcription-PCR and real-time-PCR data. To determine the specific expression sites of MMP-9 in the bovine testes, immunohistochemistry was performed. Expression of MMP-9 was observed in cells near the basement membrane of seminiferous tubules in both 5- and 11-month old testes. Furthermore, MMP-9 positive cells expressed protein gene product 9.5 (PGP9.5) and deleted in azoospermia (DAZL) that are already known as bovine spermatogonial stem cells markers. In the present study, MMP-9 expression was identified in both pre- and post-pubertal bovine spermatogonia expressing PGP9.5 and DAZL, and located near the basement membrane of seminiferous tubules. Thus, MMP-9 can be used as a marker for bovine spermatogonia, and may provide useful platforms for understanding the interaction between germ cells and extracellular matrix during spermatogenesis in the seminiferous tubules.