The characterization of fish blood proteomes is important for the comparative studies of seminal and blood proteins as well as for the analysis of fish immune mechanisms and pathways. In this study LC-MS/MS and 2D DIGE was applied to compare seminal and blood plasma trout proteomes. The 54 differentially abundant proteins identified in seminal plasma are involved in a variety of signaling pathways, including protein ubiqutination, liver X receptor/retinoid X receptor (LXR/RXR) and farnesoid X (FXR)/RXR activation, cell cycle and acute phase signaling. These finding may indicate the prevalence of acute phase signaling pathways in trout seminal plasma, and its essential role in protecting spermatozoa and reproductive tissues. Furthermore our study provides the first in-depth analysis of the rainbow trout blood plasma proteome, with a total of 119 identified proteins. The major proteins of rainbow trout blood plasma were recognized as acute phase proteins. The Ingenuity Pathway Analysis of trout BP plasma proteins indicated that acute phase response signaling, complement system, LXR, FXR-RXR activation and coagulation system are the top canonical pathways associated with trout blood proteins. In conclusion this study enhances the knowledge of the blood origin of trout seminal plasma proteins and the understanding of fish reproductive biology. Additionally our results provide new insight into blood proteins specifically important for fish physiology and innate immunity.