Altered gut microbiota is associated with autism spectrum disorders (ASD), a group of complex, fast growing but difficult-to-diagnose neurodevelopmental disorders worldwide. However, the role of the oral microbiota in ASD remains unexplored. Via high-throughput sequencing of 111 oral samples in 32 children with ASD and 27 healthy controls, we demonstrated that the salivary and dental microbiota of ASD patients were highly distinct from those of healthy individuals. Lower bacterial diversity was observed in ASD children compared to controls, especially in dental samples. Also, principal coordinate analysis revealed divergences between ASD patients and controls. Moreover, pathogens such as Haemophilus in saliva and Streptococcus in plaques showed significantly higher abundance in ASD patients, whereas commensals such as Prevotella, Selenomonas, Actinomyces, Porphyromonas, and Fusobacterium were reduced. Specifically, an overt depletion of Prevotellaceae co-occurrence network in ASD patients was obtained in dental plaques. The distinguishable bacteria were also correlated with clinical indices, reflecting disease severity and the oral health status (i.e. dental caries). Finally, diagnostic models based on key microbes were constructed, with 96.3% accuracy in saliva. Taken together, this study characterized the habitat-specific profile of the oral microbiota in ASD patients, which might help develop novel strategies for the diagnosis of ASD.