3' end processing of messenger RNAs (mRNAs) is not only an essential step in eukaryotic gene expression, but it also impacts many other aspects of mRNA maturation and decay. A large portion of eukaryotic genes produce multiple mRNAs with different 3' ends through alternative cleavage/polyadenylation (APA). mRNA 3' processing and especially APA has been increasingly recognized as an important mechanism for gene regulation. Much of what we currently know about eukaryotic mRNA 3' processing came from studies using the genetically tractable yeast systems. Here we review the fungal mRNA 3' processing system by describing both the evolutionarily conserved mechanisms as well as the fungus-specific features.