Sexual reproduction in fungi relies on proteins with well-known functions encoded at the mating type (MAT) loci. In the Basidiomycota, MAT loci are often bipartite, the P/R locus encoding pheromone precursors and pheromone receptors and the HD locus encoding heterodimerizing homeodomain transcription factors (Hd1 and Hd2). The interplay between different alleles of these genes within a single species determines a variety of sexual systems and patterns, which may result in the emergence of hundreds of compatible mating types. However, a minority of species are homothallic, reproducing sexually without the need for a compatible partner. Here we examine the organization and function of the MAT loci of Cystofilobasidium capitatum, a species in the order Cystofilobasidiales, which is unusually rich in homothallic species. For this, we determined MAT gene content and organization in C. capitatum and found that it resembled a mating type of the closely related heterothallic species Cystofilobasidium ferigula. To explain the homothallic sexual reproduction observed in C. capitatum we examined HD -protein interactions in the two individual Cystofilobasidium species and determined C. capitatum MAT gene expression both in the natural setting and upon heterologous expression in Phaffia rhodozyma, a homothallic species belonging to a clade sister to the Cystofilobasidium. We conclude that the molecular basis for homothallism in C. capitatum appears to be distinct from that previously established for P. rhodozyma. Unlike the latter species, homothallism in C. capitatum may involve constitutive activation or dispensability of the pheromone receptor and the functional replacement of the usual Hd1/Hd2 heterodimer by an Hd2 homodimer. Overall, our results suggest that homothallism evolved multiple times in the Cystofilobasidiales, underpinned by diverse molecular mechanisms.