Endophytic Bacillus and Pseudomonas genera have been reported in different plant tissues (1, 2). Several members of these genera possess functions related to plant growth-promoting rhizobacteria (PGPR), such as nutrient solubilization, hormone modulation, and antimicrobial activities (3, 4). Scientific evidence suggests that endophytes are influenced by the host plant’s chemical profile (5). Consequently, medicinal plants exhibiting diverse and potent chemical compounds potentially harbor endophytes with unexplored bioactive properties (6, 7). Endophytic communities of Cannabis sativa (cannabis) and Chelidonium majus (greater celandine) remain underexplored, particularly in terms of functional properties related to plant growth promotion and disease suppression. Hence, this study reports bacterial endophytes isolated from C. sativa and C. majus, which were provided by a commercial grower in Quebec, Canada. Plant materials were surface sterilized by immersion in hydrogen peroxide (30% w/w) for 7 min, followed by three 5-min rinses in sterile water, and sterility was confirmed by imprinting onto Luria–Bertani (LB) agar. The plant materials were then aseptically sectioned, incubated in sterile water for 20 min, serially diluted (10⁻¹ and 10⁻³), and plated on LB and nutrient agar supplemented with 1% sucrose and 10 µg/mL Benomyl. Colonies were selected based on distinct morphology, followed by repeated subculturing to obtain pure isolates. A single colony from each isolate was inoculated into 15 mL of LB broth and incubated overnight at 35°C with shaking at 180 rpm. Genomic DNA was extracted from pelleted cells using the DNeasy Blood and Tissue Kit (Qiagen, Germany), following the manufacturer’s protocol. Sequenced 16S amplicons produced with universal primers 27F/534R (8) were putatively identified by BLAST. Seven Bacillus strains (BS-114, BS-115, BS-116, BS-118, BSM-119, BS-120, and BS-121) isolated from Chelidonium majus seeds and six Pseudomonas strains isolated from Cannabis sativa roots (PF-1, PPW-26, PFM-34, and PFM-48) and stems (PF-69 and PS-72) were reported. Whole genome sequencing of these strains was performed by Day Zero Diagnostics (MA, USA). Library preparation, DNA fragmentation, and barcode attachment were performed using transposase-based tagmentation with the Rapid Barcoding Sequencing Kit (SQK-RBK114.96), followed by cleanup and size selection (≥150 bp) using solid-phase reversible immobilization (SPRI) beads. Long-read sequencing was performed using the PromethION-24 platform with the FLO-PRO114M flow cell, and quality was monitored by the MiniKNOW interface from Oxford Nanopore Technologies (ONT). Base calling and demultiplexing were conducted using Guppy v.6.5.7 (ONT) (9). Quality control involved down-sampling reads to 500–1,500 Mb per sample, followed by trimming and filtering with Fastp v.0.23.2. (10). Trimmed and filtered reads were assembled de novo with Flye v.2.9.2 (11) using the --nano-hq and—meta parameters. Assembly quality was assessed with QUAST, excluding short contigs (<500 bp) and those with low depth (<5×). The resulting assemblies were annotated using NCBI’s PGAP. Taxonomic assignments were based on NCBI annotation and sequence similarity, with organisms reported at the genus level and, where supported, at the species level. Strain typing was conducted in silico using the PubMLST database. Detailed genome assembly statistics are provided in Table 1. Default parameters were used for all programs unless otherwise specified.