Abstract Phytobiomes consist of plants, their environment, and their associated communities of macro and microorganisms. Within the phytobiome, the microbiome consists of the microorganisms associated with the plants comprising the endophytes and epiphytes. Endophytes are microorganisms, mainly consisting of bacteria and fungi, which colonise internal plant tissues without causing any disease symptom or tissue damage in different hosts. All these organisms associated to the plant contribute to its fitness. In this article, we revised a total of 103 studies containing the terms phytobiomes and microbiomes and endophytes, with the aims of reviewing: (i) the evolution of the term endophyte and the evolution of the endophyte condition; (ii) the current literature on studies considering the endophyte community within phytobiomes; and (iii) the literature on the bacteria living in fungal endophytes. In our analyses, we highlighted the biases that have been introduced in the phytobiomes' studies. For example, the presence of endohyphal bacteria could have contributed to overestimating the number of bacterial endophytes in the scientific literature. This is the first article that includes studies that evaluate endophytes that are not considered alone but belonging to a complex interacting community, the phytobiome.