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Orchidaceae is one of the largest flowering plant families of the plant kingdom. The habitats of orchids are highly diverse, ranging from tree bark and damp forest floors to rock crevices, sandy dunes and semi-arid deserts. The diversity of endophytes (internal symbiotic fungi) associated with orchids is enormous. Most studies of endophytic fungi from orchids in the past have focused on mycorrhizal endophytes (internal symbiotic fungi associated with plant roots). There has, however, been an increasing trend to study non-mycorrhizal endophytes from orchids because of their physiological roles and their potential as sources of novel bioactive compounds. This review discusses the methods used in the isolation and identification of endophytic fungi from orchids, their diversity and host-specificity, their significance in orchid conservation and cultivation, and their potential application in the discovery of bioactive compounds.