IntroductionTicks and fleas, as blood-sucking arthropods, carry and transmit various zoonotic diseases. In the natural plague foci of China, monitoring ofYersinia pestishas been continuously conducted inMarmota himalayanaand other host animals, whereas other pathogens carried by vectors are rarely concerned in the Qinghai-Tibet Plateau.MethodsIn this study, we investigated the microbiota of ticks and fleas sampling fromM. himalayanain theQinghai-TibetPlateau, China by metataxonomics combined with metagenomic methods.ResultsBy metataxonomic approach based on full-length 16S rDNA amplicon sequencing and operational phylogenetic unit (OPU) analyses, we described the microbiota community of ticks and fleas at the species level, annotated 1,250 OPUs in ticks, including 556 known species and 492 potentially new species, accounting for 48.50% and 41.71% of the total reads in ticks, respectively. A total of 689 OPUs were detected in fleas, consisting of 277 known species (40.62% of the total reads in fleas) and 294 potentially new species (56.88%). At the dominant species categories, we detected theAnaplasma phagocytophilum(OPU 421) and potentially pathogenic new species ofWolbachia, Ehrlichia, Rickettsia, andBartonella. Using shotgun sequencing, we obtained 10 metagenomic assembled genomes (MAGs) from vector samples, including a known species (Providencia heimbachaeDFT2), and six new species affliated to four known genera, i.e.,Wolbachia, Mumia, Bartonella, andAnaplasma. By the phylogenetic analyses based on full-length 16S rRNA genes and core genes, we identified that ticks harbored pathogenicA. phagocytophilum. Moreover, these potentially pathogenic novel species were more closely related toEhrlichia muris, Ehrlichia murissubsp.eauclairensis, Bartonella rochalimae, andRickettsia limoniae, respectively. The OPU 422 Ehrlichia sp1 was most related toEhrlichia murisandEhrlichia muris subsp. eauclairensis. The OPU 230Bartonellasp1 andBartonellaspp. (DTF8 and DTF9) was clustered withBartonella rochalimae. The OPU 427Rickettsiasp1 was clustered withRickettsia limoniae.DiscussionThe findings of the study have advanced our understanding of the potential pathogen groups of vectors in marmot (Marmota himalayana) in the Qinghai-Tibet Plateau.