Fungi (Eumycota) form close associations with plants, with which they have co‐existed since the dawn of life on land, but their diversity in early terrestrial ecosystems is still poorly understood. We studied petrographic sections of exceptionally well‐preserved petrified plants from the 407 million yr‐old Rhynie Chert (Scotland, UK). For comparative purposes, we illustrate fungal associations in four extant lower land plants. We document two new endophytes in the plant Horneophyton lignieri: Palaeoglomus boullardii (sp. nov. Glomeromycota) colonizes parenchyma in a discontinuous zone of the outer cortex of the aerial axes, forming arbuscule‐like structures, vesicles and spores; Palaeoendogone gwynne‐vaughaniae (gen. nov., sp. nov. Mucoromycotina) colonizes parenchyma in the basal part of the plant, where it is present in intercellular spaces and as intracellular coils but absent from rhizoids. Critical comparisons between the newly discovered Horneophyton endophytes, fungi previously described from the Rhynie Chert and fungal colonization in extant lower land plants reveal several features characteristic of both Mucoromycotina and Glomeromycota. A reappraisal of fungal associations in early land plants indicates that they are more diverse than assumed hitherto, overturning the long‐held paradigm that the early endophytes were exclusively Glomeromycota.