Abstract The opportunistic pathogen Cryptococcus neoformans adapts to diverse host microenvironments during infection, yet the contribution of epigenetic mechanisms remains unclear. Comparative genomics across 50 basidiomycete species revealed that one chromatin protein, the linker histone H1, is uniquely duplicated across the entire Cryptococcus genus , generating paralogs H1.51 and H1.52 with divergent evolutionary trajectories. Molecular evolution analyses revealed that H1.51 experienced inte