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Mitogen activated protein kinase kinase (MKK) 3 and 6 are the main p38 mitogen-activated protein kinase activators in mammals. In the present study, three Atlantic salmon MKK6 orthologs were identified. The deduced amino acid sequences of the salmon MKK6 proteins were highly similar to mammalian MKK6 sequences, and they were ubiquitously expressed. All three were shown to be upstream activators of salmon p38. In cells exposed to sorbitol, sodium arsenite and UV radiation, the different salmon MKK6s were shown to be selectively activated. Thus, our results suggest a specific function of the three salmon MKK6s depending on which stress stimuli the cells are exposed to. Phylogenetic analysis of MKK6 and MKK3 sequences from different species indicate that salmon is unique in having three MKK6 gene copies, whereas other fish species possess one or two MKK6 genes. Interestingly, in contrast to mammals, fish do not have an MKK3 gene. We propose that two major duplication events have occurred for the ancestral MKK3/6 gene: one in tetrapods yielding MKK3 and MKK6, and another one in fish yielding two MKK6 paralogs. The third MKK6 copy found in salmon is probably the result of the salmonid-specific tetraploidization event. In conclusion, we report for the first time in any species the existence of three MKK6 genes displaying distinct expression and activation patterns. Furthermore, MKK3 is dispensable in some vertebrates because it is absent from fish genomes despite being present in chicken and all mammals sequenced so far.