In the majority of diploid eukaryotes, each meiotic process generates four haploid gametes with each containing a single recombinant nucleus. In some species and/or some meiotic processes, aneuploid or diploid gametes can also be generated due to chromosomal non-disjunction and/or the co-packaging of two of the four haploid nuclei into the same gamete. Here we show that another process is involved in generating genotypes of sexual progeny from a hybrid cross between two divergent lineages of the human fungal pathogen Cryptococcus neoformans. Through micro-dissection of 1358 basidiospores from 194 basidia and genotyping using 33 co-dominant genetic markers, the genotypes of all 230 germinated basidiospores from 94 basidia were obtained. The minimum haploid genotypes required to constitute the observed genotypes from each basidium were then inferred. Our results demonstrated that more than four haploid nuclear genotypes are required to explain the observed genotypes of basidiospores in seven of the 94 basidia. Our results suggest that mitotic recombination within basidia must be involved to produce the observed genotypes in these seven basidia. The mitotic recombination likely includes both chromosomal loss and crossing over. This novel recombination process could play an important role in generating the genotypic and phenotypic diversities of this important human pathogen.