Cryptococcus neoformans is an unconventional dimorphic fungus that can grow either as a yeast or in a filamentous form. To facilitate investigation of genetic factors important for its morphogenesis and pathogenicity, congenic a and α strains for a filamentous form were constructed. XL280 (α) was selected as the background strain because of its robust ability to undergo the morphological transition from yeast to the filamentous form. The MATa allele from a sequenced strain JEC20 was introgressed into the XL280 background to generate the congenic a and α pair strains. The resulting congenic strains were then used to test the impact of mating type on virulence. In both the inhalation and the intravenous infection models of murine cryptococcosis, the congenic a and α strains displayed comparable levels of high virulence. The a-α coinfections displayed equivalent virulence to the individual a or α infections in both animal models. Further analyses of the mating type distribution in a-α coinfected mice suggested no influence of a-α interactions on cryptococcal neurotropism, irrespective of the route of inoculation. Furthermore, deletion or overexpression of a known transcription factor, Znf2, in XL280 abolished or enhanced filamentation and biofilm formation, consistent with its established role. Overexpression of Znf2 in XL280 led to attenuation of virulence and a reduced abundance in the brain but not in other organs, suggesting that Znf2 might interfere with cryptococcal neurotropism upon extrapulmonary dissemination. In summary, the congenic strains provide a new resource for the exploration of the relationship in Cryptococcus between cellular morphology and pathogenesis.