Darwinian selection approach is widely adopted from single coding gene comparisons to whole genome investigations, to trace the evolutionary forces affecting shape and function of several molecular traits. Positive selection has been demonstrated to drive an enhanced evolution and promote rapid divergence in several genes as in immune defense, host pathogen recognition and reproductive proteins. On the contrary, purifying selection opposes to gene mutations preserving the functional constraints and the molecular architecture, as in housekeeping genes or in trans-membrane protein domains. With the goal of analyzing the natural selection forces which have driven the molecular adaptation of respiratory proteins we have comparatively evaluated 17 groups of non-vertebrate oxygen transporters. The results show a wide dominance of purifying selection in almost all protein families, suggesting that the structural and functional constraints required for the reversible oxygen binding are strictly conserved during evolution. The single exception is constituted by crustacean hemocyanin for which the analyses reveal several sites under diversifying selection. The structural and functional heterogeneity of crustacean hemocyanin is considered to be the result of a complex evolutionary process originated from the aggregation of simpler molecules. The hemocyanins existing today have been created by the gene fusion of ancestral proteins, which constitute the actual three domains and which share, in the new molecule, their ancestral biological functions. Besides to the oxygen binding, achieved by the highly conserved active site, arthropod hemocyanins contribute to other physiological processes, like immune response to pathogens, phenoloxidase activity, wound repair and molting. Furthermore, the analysis of selecting forces, acting on all available genes of the crustacean hemocyanins reveal a complex pattern of accelerated evolution events occurred after gene duplication followed by the firm dominance of negative selection. This fact leads the consideration that the crustacean hemocyanin heterogeneity at the level of higher taxa is a consequence of accelerated evolution, succeeding ancestral episode of gene duplication, and support the diversification of structures and the acquisition of new functions showed by crustacean hemocyanin in a context of adaptive evolution.