In petroleum production, microbial investigations are essential for microbial-induced corrosion (MIC) control and enhanced oil recovery (EOR) processes. It is suggested that microorganisms can attach to the inner wall of pipes as biofilms, which are more stable and could cause more serious corrosion than planktonic microorganisms in the water phase. At present, research on the biofilms during oil production is mainly focused on the surface pipelines, while few reports have directly investigated biofilms in vertical deep wells. Therefore, in this study, wellbore biofilms were sampled during well workover from several well-tube segments corresponding to different original depths (approximately 0, 840, and 1330 m). The injected water was sampled as well. The results of the 16S rRNA gene library sequencing showed that the biofilms and water-phase communities were distinct (dissimilarity of 0.56-0.64), although they shared 64 OTUs. At the phylum level, the relative abundance of Proteobacteria was 74.65% in the water phase and only 7.86-27.41% in the biofilms. The dominant phylum, Firmicutes, was 6.03-41.21% in the three biofilms, while only 1.16% in the water phase. With increasing depth, the biofilm communities became more diverse (Shannon index of 3.43-4.21), more anaerobic, and more thermophilic possibly due to the depleting oxygen and increasing temperature in samples from the deeper well. For instance, the relative abundance of anaerobes (archaea and strict anaerobic bacteria) in biofilms increased from 18.32 to 40.53%. Thermophilic bacteria (such as Kosmotoga) increased from 6.65 to 15.82%. Among methanogens, hydrogenotrophic genera (such as Methanobacterium and Methanolinea) increased from 3.66 to 9.68%. This study revealed the structural differences between water-phase and biofilm communities in the well, and the depth-dependent distribution of the biofilm communities. These results improved the understanding of microbial ecology in wellbores, which will benefit microbial activity control measures applied in oil production processes, including MIC and oil recovery.