<p><strong>Background</strong>: <em>Pasteuria penetrans</em> is a nonculturable bacterium that obligately parasitizes several species of phytopathogenic nematodes. Unknown endogenous female, plant or microbial reproductive factors are indispensable for multiplication and endospore formation of <em>P. penetrans</em>. <strong>Objective</strong>: To characterize <em>P. penetrans</em> endospores by 16S rRNA gene sequencing in samples from infected adult female <em>Meloidogyne javanica</em> and microbiota of infected and uninfected adult female <em>M. javanica</em> with <em>P. penetrans</em> by high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene. <strong>Methodology</strong>: Infected roots were collected from grapevines; fresh infective juvenile nematodes (J2) were extracted for <em>P. penetrans</em> endospore fixation and inoculation into tomato plants. Genomic and metagenomic DNA from infected and uninfected adult females of <em>M. javanica</em> was extracted for sequencing by sequencing the V4 region of the 16S rRNA gene of <em>P. penetrans</em> and its bacterial microbiome. The generated sequences were processed using bioinformatics software for analyses of alpha and beta diversity indices of the bacterial microbiome. <strong>Results</strong>: An amplicon of 550 base pairs with 98% identity and homology to <em>P. penetrans</em> was obtained. The taxonomic profile revealed the highest bacterial diversity and richness in the microbiota related to infected adult females, with <em>Proteobacteria</em> occurring in both samples between 45 and 83%, followed by <em>Firmicutes</em>, <em>Actinobacteria</em> and <em>Bacteroidetes</em> with 19, 11 and 8% respectively at the phylum level. Likewise, the most abundant genera associated with the native microbiota of the adult nematode were identified as <em>Pseudomonas</em>, <em>Flavobacterium</em> and <em>Chitinophaga</em> at 82.5, 15 and 2%, respectively. In infected females, <em>Paenibacillus</em>, <em>Pasteuria</em>, <em>Pseudomonas</em> and <em>Streptomyces</em> were recorded with 45, 7, 6 and 5% respectively, the most abundant. <strong>Implications</strong>: The results suggest the existence of bacterial genera in infected <em>M. javanica</em> females involved in the in vivo development of <em>P. penetrans</em> endospores. <strong>Conclusions</strong>: This would reveal a reduction of <em>Pseudomonas</em> dominance favoring the colonization of different bacteria that cohabit with <em>P. penetrans</em>, being this change in the microbial composition a possible factor that favors the multiplication of <em>P. penetrans</em> endospores within the host.</p>