Rastrelliger brachysoma is a mariculture candidate species, but reproduction in captive fish has been problematic. This report examines the difference in the HPG axis, the neuroendocrine system and the development of reproductive tissues between captive vs. wild male R. brachysoma. The gonadosomatic index (GSI) of sexually mature male wild R. brachysoma was 1.12±0.34 and 1.94±0.26 during the non-breeding and breeding seasons, respectively. Captive R. brachysoma had a GSI of 1.88±0.17. All wild R. brachysoma were in the late spermatogenic stage irrespective of seasons. Immunostaining results showed that sbGnRH-immunoreactive neurons were distributed in three areas of the brain, namely the nucleus periventricularis, nucleus preopticus and nucleus lateralis tuberis. Follicle stimulating hormone and luteinizing hormone immunoreactivities were also observed in the pituitary gland. The levels of brain sbGnRH and GtH mRNA were not significantly different between the non-breeding and breeding seasons, but captive fish displayed (times or percent difference) lower mRNA levels than wild fish. These results suggest that these hormones control the testicular development in R. brachysoma and that the impaired reproduction in captivity may be due to their relative lower expression levels of follicle stimulating hormone and luteinizing hormone genes.