The spleen plays a crucial role in innate and adaptive immunity in bony fish. Consequently, this organ is well suited to assess the immune competence of an organism and hence provides useful information for comparison and classification of production traits of food fish, such as robustness and susceptibility. To gain information about differences in the basal splenic transcriptome activity, healthy rainbow trout of the commercially important strain TCO and the local selection strain BORN have been compared in a holistic expression analysis using the GRASP 16K cDNA microarray. Nearly all differentially expressed genes (n = 807) in the spleen were on a lower expression level (n = 802) in BORN trout compared to the TCO strain. Global gene ontology analysis revealed that most genes are involved in fundamental biological processes like cellular growth, vesicular trafficking and energy metabolism. Surprisingly, only 7 % of splenic differentially expressed genes are associated with functions of the immune system like TLR signaling, acute phase response and complement system. MARCH3 is one lower expressed gene of interest in BORN trout. This gene, coding for an E3 ubiquitin ligase, is involved in three metabolic functions: immune system, vesicular trafficking and ubiquitination. Since MARCH genes are furthermore differently regulated in the two strains after viral infection and assumed to be potentially active in regulation of immune receptors in fish, MARCH3 was chosen for a closer structural analysis. In concert with the data interpretation of the achieved comparative transcriptome analysis for the involved rainbow trout strains, we provide the full mRNA sequence of trout MARCH3 and its hypothetical protein structure.