Follicle-stimulating hormone (Fsh) modulates fish spermatogenesis in a steroid-independent manner by modulating the expression of growth factors controlling spermatogonial proliferation and differentiation. Here, we find that two of these Fsh-responsive growth factors influence each other’s activity on zebrafish spermatogonia: anti-Müllerian hormone (Amh) and the insulin-like growth factor 3 (Igf3). Fsh-time and -dose response experiments ex vivo demonstrate that igf3 transcript levels are rapidly up-regulated, remain elevated, and respond to lower Fsh concentrations than are required to decrease amh mRNA levels. Immunofluorescence studies suggest that Fsh also decreases Amh protein levels while increases in Igf3 protein levels were comparatively small. Zebrafish Amh compromised Igf3-induced proliferation of type A undifferentiated (Aund) and type A differentiating (Adiff) spermatogonia. Proliferation of Sertoli cells associated with type Aund spermatogonia was also reduced by Amh. To better understand the inhibitory effects of Amh on germ cell development, we investigated Amh-induced changes in zebrafish testicular gene expression by RNAseq. Analyzing the differentially expressed genes demonstrates that several signaling pathways are potentially involved in mediating the inhibitory activity of Amh. The majority of the genes identified were down-regulated, such as the transcript levels of igf3, insl3 and of steroidogenesis-related genes, all three stimulating germ cell differentiation. At the same time, Amh increased the expression of inhibitory signals, such as inha and id3 transcript levels. Altogether, our results provide new information on how Fsh regulates zebrafish spermatogenesis by orchestrating the actions of different growth factors and other paracrine signaling systems, including the control of the multiple inhibitory effects of Amh.