The mating types in Ogataea polymorpha are dictated by the expression of transcription factors MATa2 or MATα1 in a and α-type cells, respectively and the mating response is activated in response to environmental stress. Although it is known that these transcription factors are essential for mating-type identity, their regulatory targets are unknown in O. polymorpha. Since using environmental stressors to induce mating does not effectively show differential gene expression between mating types, we used a more direct approach by inducing a key regulator of mating, STE12. STE12 is a sequence-specific transcription factor that is activated by environmental stressors (nitrogen deprivation) in O. polymorpha and as such is responsible for inducing the expression of mating genes. In order to manipulate the mating response for experimentation, the expression of STE12 was put under the control of an inducible promoter and overexpressed in both wildtype strains and strains that had either MATa2 or MATα1 deletions. Total RNA-seq analyses compared the RNA expression of deletion strains to control strains and the differential gene expression between the two revealed the regulatory targets of the MAT transcription factors. Many of the mating-type specific genes were involved in the mating-type specific pheromone response pathway and the haploid specific genes were a part of a more general pheromone response pathway. By studying the mating-type specific gene expression in O. polymorpha, we can better understand not only how cells are different within a species but also between species through comparison of their mating-type specific genes. Since speciation relies on sexual barriers to separate species, comparing how mating-type specific genes are different and used differently between yeast species helps us better understand how these species became sexually isolated and how new species are created as a result.