In mycorrhizal associations, water transport properties of the fungal hyphae may have a profound effect on water transport of the host plant. The importance of aquaporins, water-transporting members of the major intrinsic protein (MIP) family, in facilitating water transport has been widely acknowledged and extensively studied in plants. However, until recently, relatively little was known about the structure, function, and regulation of fungal MIPs. The rapid increase in the number of sequenced fungal genomes, including Laccaria bicolor and other mycorrhizal fungi, has enabled functional and comparative genomic investigations to delineate the role that fungal MIPs play in mycorrhizal-facilitated plant water transport. Phylogenic analysis of 229 fungal MIPs from 88 species revealed that MIPs of mycorrhizal fungal species fall into four clusters delineated by functionally characterized fungal MIPs: the orthodox aquaporins, the aquaglyceroporins, the facultative fungal aquaporins, and the X intrinsic proteins. This comparative genomics analysis, together with in silico structural characterization of predicted MIPs and recently published functional characterization of MIPs from a small number of ectomycorrhizal and arbuscular mycorrhizal species, provide new insight into MIP gene families of mycorrhizal fungi and possible roles for fungal aquaporins in water relations of mycorrhizal plant-fungus symbioses.