Cryptococcus neoformans (Cn) contains two ubiquitin (UBI)-encoding genes located on separate chromosomes. The UBI1 gene consists of UBI fused to a 53-amino-acid (aa) tail and is 95% identical to the Saccharomyces cerevisiae (Sc) UBI1 which codes for an UBI-CEP52 ribosomal protein fusion. UBI4 is a polyubiquitin gene that contains five UBI repeats. The UBI4 aa sequences differ from Sc UBI by a single aa. UBI1 contains two introns in the UBI-encoding portion and two introns in the tail. Single introns are present in three of the repeats in UB14 and are located at the same positions as those in UBII. There was also an average of 15% nt differences among UBI repeats. The results provide evidence of extensive recombination and/or conversion events between repeated genes in Cn.