BackgroundHuntiellaresides in the Ceratocystidaceae, a family of fungi that accommodates important plant pathogens and insect-associated saprotrophs. Species in the genus have either heterothallic or unisexual (a form of homothallism) mating systems, providing an opportunity to investigate the genetic mechanisms that enable transitions between reproductive strategies in related species. Two newly sequencedHuntiellagenomes are introduced in this study and comparative genomics and transcriptomics tools are used to investigate the differences between heterothallism and unisexuality across the genus.ResultsHeterothallic species harbored up to seven copies of the a-factor pheromone, each of which possessed numerous mature peptide repeats. In comparison, unisexualHuntiellaspecies had only two or three copies of this gene, each with fewer repeats. Similarly, while the heterothallic species expressed up to 12 copies of the mature α-factor pheromone, unisexual species had up to six copies. These significant differences imply that unisexualHuntiellaspecies do not rely on a mating partner recognition system in the same way that heterothallic fungi do.ConclusionWhile it is suspected that mating type-independent pheromone expression is the mechanism allowing for unisexual reproduction inHuntiellaspecies, our results suggest that the transition to unisexuality may also have been associated with changes in the genes governing the pheromone pathway. While these results are specifically related toHuntiella, they provide clues leading to a better understanding of sexual reproduction and the fluidity of mating strategies in fungi more broadly.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09355-9.