Fungi are an essential component of any ecosystem and have diverse ecological roles, ranging from endophytes to epiphytes and pathogens to saprobes. The current estimate of fungal endophytes is around 1 million species, however, we estimate that there is likely over 3 million species and only about 150,000 fungal species have been named and classified to date. Endophytes inhabit internal plant tissues without causing apparent harm to the hosts. Endophytes occur in almost every plant from the coldest climates to the tropics. They are thought to provide several benefits to host plants and improve the hosts’ ability to tolerate several abiotic and biotic stresses. Endophytes produce secondary metabolites with biotechnological, industrial and pharmaceutical application. Some endophytes appear to be host-specific, while some are associated with a wide range of hosts. We discuss the importance of endophytes. The ability to switch lifestyles from endophytes to pathogens or saprobes is discussed. Interactions between endophytes and hosts based on fossil data is also highlighted. Factors that influence the specificity in endophytes are discussed. We argue that the endophytic lifestyle is a common strategy in most fungi and that all fungi have endophytic ancestors. We critically evaluate the influence of co-evolution based on fossil data. We hypothesise the influence of specificity on the estimated number of endophytes and overall species numbers, and present examples of metabolites that they produce. We argue that studying endophytes for novel compounds has limitations as the genera recovered are limited. However, if saprobes were chosen instead, this would result in a much higher species diversity and undoubtedly chemical diversity.

真菌是任何生态系统的重要组成部分，具有多种生态作用，从内生菌到附生菌，从病原体到腐生菌。目前估计内生真菌约有 100 万种，但我们估计可能超过 300 万种，而迄今为止只有约 150,000 种真菌被命名和分类。内生菌栖息在植物内部组织中，不会对宿主造成明显的伤害。从最寒冷的气候到热带地区，几乎所有植物中都存在内生菌。它们被认为可以为寄主植物提供多种益处，并提高寄主耐受多种非生物和生物胁迫的能力。内生菌产生具有生物技术、工业和制药应用的次生代谢产物。一些内生菌似乎具有宿主特异性，而另一些则与广泛的宿主相关。我们讨论内生菌的重要性。讨论了将生活方式从内生菌转变为病原体或腐生菌的能力。还强调了基于化石数据的内生菌和宿主之间的相互作用。讨论了影响内生菌特异性的因素。我们认为内生生活方式是大多数真菌的常见策略，并且所有真菌都有内生祖先。我们根据化石数据批判性地评估共同进化的影响。我们假设特异性对内生菌估计数量和物种总数的影响，并提供它们产生的代谢物的例子。我们认为，研究内生菌中的新化合物具有局限性，因为回收的属是有限的。然而，如果选择腐生，这将导致更高的物种多样性和毫无疑问的化学多样性。