Thelastomatid nematodes (Nematoda: Oxyurida: Thelastomatoidea) are obligatory parasites that occur naturally in the hindgut of arthropods. Their origin and impact in the host is still unknown. Previous studies showed that the presence of thelastomatid nematodes in the gut of cockroaches (Periplaneta fuliginosa and P. americana) could influence the composition of their hindgut microflora. Through a metagenomic approach (16S rRNA V3-V4 sequencing), we have characterized the hindgut microbiome of P. japonica in the presence of thelastomatid nematodes (L1986, natural parasitic nematode Protrellus sp. present as a natural infection condition; and L1987, non-native parasitic nematode Leidynema appendiculatum present as an artificial infection condition). The hindgut microbiome of P. japonica in both conditions were mainly composed of Bacteroidetes, Firmicutes and Proteobacteria. Moreover, the natural and artificial infection by thelastomatid nematodes lead to shifts in the relative abundance of these main resident flora as seen in P. americana. The OTUs percentage of Bacteroidetes and Proteobacteria were higher in P. japonica infected with Protrellus sp. (L1986) than in P. japonica infected by L. appendiculatum (L1987), while OTUs from Firmicutes phylum was higher in L1987 than in L1986. This study fosters a detailed investigation in the role played by these animal parasites in their host insect.