The bacterial community associated with a full scale autothermal thermophilic aerobic digester (ATAD) treating sludge, originating from domestic wastewater and destined for land spread, was analysed using a number of molecular approaches optimised specifically for this high temperature environment. 16S rDNA genes were amplified directly from sludge with universally conserved and Bacteria-specific rDNA gene primers and a clone library constructed that corresponded to the late thermophilic stage (t = 23 h) of the ATAD process. Sequence analyses revealed various 16S rDNA gene sequence types reflective of high bacterial community diversity. Members of the bacterial community included α- and β-Proteobacteria, Actinobacteria with High G + C content and Gram-Positive bacteria with a prevalence of the Firmicutes (Low G + C) division (class Clostridia and Bacillus). Most of the ATAD clones showed affiliation with bacterial species previously isolated or detected in other elevated temperature environments, at alkaline pH, or in cellulose rich environments. Several phylotypes associated with Fe(III)- and Mn(IV)-reducing anaerobes were also detected. The presence of anaerobes was of interest in such large scale systems where sub-optimal aeration and mixing is often the norm while the presence of large amounts of capnophiles suggest the possibility of limited convection and entrapment of CO2 within the sludge matrix during digestion. Comparative analysis with organism identified in other ATAD systems revealed significant differences based on optimised techniques. The abundance of thermophilic, alkalophilic and cellulose-degrading phylotypes suggests that these organisms are responsible for maintaining the elevated temperature at the later stages of the ATAD process. ► Phylogeny presented based on optimised niche specific molecular tools. ► ATAD contains large numbers symbionts, capnophiles and anaerobes. ► Alkalophilic cellulolytic phylotypes are keys to stability of elevated temperature. ► Dataset may have utility in bioaugmentation for improvement of ATAD sludge settling. ► Great dissimilarity in microorganisms between worldwide ATAD systems.