Microbes that reside within cannabis tissues (endophytes) are thought to provide benefits to the plant although their presence has also raised concerns about possible negative impacts on plant quality. To determine the nature of these endophytes and their potential impact on cannabis growth, tissues of high THC-containing plants were subjected to Next-Generation Sequencing (NGS). Reads were classified using a metagenomics classification algorithm that assigns a taxonomic identification to each sequencing read and estimates the abundance of each species in the sample. The tissues analyzed included 90 samples of roots, stems, leaves and flowers representing 12 genotypes. A few seed samples were also included. Scanning electron microscopic studies were performed on stem tissues to examine the xylem and pith tissues for presence of endophytes. Up to 20 genera of fungi, 9 yeasts and 18 bacterial genera were present at varying frequencies (percent of total reads of the taxon relative to total reads of that microbe group) in the tissues. The highest frequencies were generally found in the roots, followed by stems. Seeds and flowers contained an abundance of endophytic and epiphytic microbes. The most frequently detected fungal genera were Penicillium, Fusarium and Rhizophagus (Glomus) while the most abundant bacterial genera were Bacillus and Pseudomonas. Penicillium chrysogenum and Fusarium oxysporum were present in all tissue samples. The microbiome of cuttings and vegetative plants mirrored that of mother plants, suggesting that transmission of endophytes was occurring through vegetative propagation. Scanning electron microscopy of sectioned stems from mother plants revealed the presence of fungal spores of a range of species within the xylem vessel elements and pith parenchyma cells. The cocofibre substrate in which mother plants were grown greatly influenced the microbes present, particularly in roots but also in other tissues. Application of biocontrol fungi, such Trichoderma harzianum, was followed by detection in roots, stems, leaves and flowers of treated plants. Applications of this biocontrol fungus to 2 week-old rooted cuttings resulted in a partial displacement of the pre-existing microbes, thus enhancing the frequency of T. harzianum in the roots but not in stems within 4 weeks after treatment. Sterilizing the cocofibre growing medium did not influence the microbiome of cuttings grown in them. Meristem tip culture eliminated almost all fungal endophytes but bacteria were still present. However, rapid recolonization by Fusarium species during the rooting phase resulted in a predominance of this pathogen in the tissues. These findings suggest that endophytic microbes are abundant in cannabis tissues and their composition is influenced by the growing substrate, as well as by applications of biocontrol agents. Meristem-derived plants should be treated with protective microbial products to occupy the biological vacuum before being used. The transmission of endophytic fungi from cannabis stems to inflorescences likely occurs and needs to be explored further.