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