The emergence of infectious diseases, particularly those caused by fungal pathogens, poses serious threats to public health, wildlife and ecosystem stability¹. Host–fungus interactions and environmental factors have been extensively examined^2,3,4. However, the role of genetic variability in pathogens is often less well-studied, even for diseases such as white-nose in bats, which has caused one of the highest disease-driven death tolls documented in nonhuman mammals⁵. Previous research on white-nose disease has primarily focused on variations in disease outcomes attributed to host traits or environmental conditions^6,7,8, but has neglected pathogen variability. Here we leverage an extensive reference collection of 5,479 fungal isolates from 27 countries to reveal that the widespread causative agent is not a single species but two sympatric cryptic species, each exhibiting host specialization. Our findings provide evidence of recombination in each species, but significant genetic differentiation across their genomes, including differences in genome organization. Both species contain geographically differentiated populations, which enabled us to identify the species introduced to North America and trace its source population to a region in Ukraine. In light of our discovery of the existence of two cryptic species of the causative agent of white-nose disease, our research underscores the need to integrate the study of pathogen variability into comprehensive disease surveillance, management and prevention strategies. This holistic approach is crucial for enhancing our understanding of diseases and implementing effective measures to prevent their spread.

传染病的出现，尤其是由真菌病原体引起的传染病，对公共卫生、野生动物和生态系统稳定构成严重威胁 ¹。宿主-真菌相互作用和环境因素已被广泛研究 ^2,3,4。然而，遗传变异在病原体中的作用往往研究较少，即使是蝙蝠白鼻等疾病也是如此，白鼻病是非人类哺乳动物中因疾病导致死亡人数最高的疾病之一 ⁵。以前关于白鼻病的研究主要集中在归因于宿主特征或环境条件的疾病结果变化 ^6,7,8，但忽略了病原体的变异性。在这里，我们利用来自 5,479 个国家/地区的 27 个真菌分离株的广泛参考集合来揭示广泛的病原体不是一个单一物种，而是两个同域隐蔽物种，每个物种都表现出宿主特化。我们的研究结果提供了每个物种重组的证据，但其基因组之间存在显着的遗传分化，包括基因组组织的差异。这两个物种都包含地理上不同的种群，这使我们能够识别引入北美的物种，并将其来源种群追溯到乌克兰的一个地区。鉴于我们发现白鼻病病原体的两种神秘物种的存在，我们的研究强调了将病原体变异性研究纳入综合疾病监测、管理和预防策略的必要性。这种整体方法对于增强我们对疾病的理解和实施有效措施来防止其传播至关重要。