Gonadotropin-releasing hormone (GnRH) plays a crucial role in regulating reproductive behavior in vertebrates through the hypothalamus-pituitary-gonad (HPG) axis. Seahorses exhibit unique male pregnancy behavior, making them an interesting subject for investigating the regulatory mechanisms behind this behavior. In this study, we focused on the lined seahorse (Hippocampus erectus) and obtained the full-length cDNA sequences of three GnRH genes: GnRH1, GnRH2, and GnRH3. Notably, we newly identified GnRH1, filling a gap in previous research that had overlooked this subtype. Through a homologous analysis, we found that the core peptide of GnRH1 in lined seahorses is not common in teleosts, while the core peptides of GnRH2 and GnRH3 are conserved. Real-time PCR was performed to determine the tissue expression patterns of these GnRH genes. Our results showed that all three genes were predominantly expressed in the brain, albeit in different regions. Specifically, GnRH1 was mainly expressed in the hypothalamus, GnRH2 in the optic tectum, and GnRH3 in the telencephalon. Expression dynamics indicated a progressive decrease in GnRH2 and a significant surge in GnRH3 during gonadal development, hinting at an alternating regulatory function. Moreover, GnRH1 and GnRH3 expression levels were considerably higher during pregnancy compared to those in pre-pregnancy and postpregnancy stages, underscoring their critical role in modulating male pregnancy behavior in lined seahorses. Our findings provide insights into the complex interplay of GnRH subtypes in regulating reproductive processes, particularly in the context of male pregnancy behavior in seahorses.