Salmonids are the most widely studied group of fish, and in the last few years, genomics technologies have begun to contribute to this rich biology. The first salmonid microarrays appeared in 2004 and since then several dozen studies have demonstrated the utility of genomic approaches. The widespread use of the genomics research on Atlantic salmon project 16 k array and greatly expanded genome resources have led to the development of an experimental 5 k oligo (70-mer) array and a 32 k cDNA microarray in the near future. In this paper, the authors examined some of the procedures used in the development of past arrays and reexamined them in light of new genomic data available. Some preliminary control experiments of the new 5 k array were investigated that examine oligo designs based on distance from the polyA tail, the effects of mismatches and cross-species hybridization specificity. Beneficial approaches are also identified in the development of the new 32 k cDNA array.