Transmembrane conductance of glycerol is typically facilitated by aquaglyceroporins (Glps), which are commonly encoded by multiple genes in metazoan organisms. To date, however, little is known concerning the evolution of Glps in Crustacea or what forces might underly such gene redundancy. Here we show that Glp evolution in Crustacea is highly divergent, ranging from single copy genes in species of tadpole shrimps, isopods, amphipods and decapods to up to 10 copies in diplostracan water fleas although with monophyletic origins in each lineage. By contrast Glp evolution in Copepoda appears to be polyphyletic, with high rates of gene duplication occurring in a genera- and species-specifc manner. Based upon functional experiments on the Glps from a parasitic copepod (Lepeophtheirus salmonis), we show that such lineage-level gene duplication and splice variation is coupled with a high rate of neofunctionalization. For L. salmonis, splice variation of a given gene resulted in tissue- or sex-specific expression of the channels, with each variant evolving unique sites for PKC or PKA regulation of intracellular membrane trafficking. The data thus reveal that mutations favouring a high fidelity control of intracellular trafficking regulation can be a selection force for the evolution and retention of multiple Glps in copepods.