[Background] Xilin river-riparian wetland-terrace grassland are the most representative aquatic-humid-terrestrial habitats in typical steppe region of Mongolia plateau, but little is known about the spatial characteristics of denitrifying bacterial communities in different habitats. [Objective] To reveal the composition, abundance, spatial distribution of denitrifying bacterial communities in different habitats of typical steppe region and associated spatial heterogeneity. [Methods] Using 454 pyrosequencing of 16S rRNA gene, we characterized community compositions and abundance of sediment/soil denitrifying bacterial communities from 6 sampling zones associated with aquatic, humid and terrestrial habitats. Based on the information of denitrifying bacterial 16S rRNA gene from previous references before 2014, we constructed denitrifying bacteria library as a reference to screen denitrifying bacterial genera associated with habitats. Meanwhile, we explored spatial heterogeneity of denitrifying bacterial genera by canonical correspondence analysis (CCA). [Results] The reference library contained 80 denitrifying bacterial species (65 genera). Accordingly, 36 denitrifying bacterial genera were screened out of total 469 bacterial genera from 6 sampling zones. Fourteen denitrifying bacterial genera co-existed in aquatic-humid-terrestrial habitats. Among them, Flavobacterium (1.65%?14.17%) and Hydrogenophaga (1.56%?1.69%) were dominant denitrifying bacteria across aquatic and humid habitats. Pseudomonas (1.85%) was the dominant bacteria only in low-floodplain wetland. The spatial distribution characteristics showed a tendency, first increased and then decreased along the aquatic-humid-terrestrial habitats, and reached peak value in low-floodplain wetland habitats. CCA analysis showed that Flavobacterium, Hydrogenophaga, Aeromonas and Sphingomonas were positively correlated with pH, water and sand contents. Whereas Bacillus, Streptomyces, Actinomadura were positively correlated with contents of clay, silt, organic matter and total nitrogen. [Conclusion] The compositions and abundance of denitrifying bacterial communities in typical steppe region showed obvious habitat heterogeneity. Low-floodplain wetland was the suitable habitat for growth and reproduction of denitrifying bacteria, which were driven by multiple environmental factors such as sediment/soil particle compositions, water content and pH.