The archaeal communities of six anaerobic granular biofilm samples were surveyed for the occurrence of Crenarchaeota, using clone library and terminal restriction fragment length polymorphism (TRFLP) analysis. One of the samples, containing a high abundance of Crenarchaeota-like organisms, was used to inoculate anaerobic reactors for the treatment of a whey-based wastewater. TRFLP was used to monitor the Crenarchaeota-like species during the trial in response to various perturbations. FISH was employed to establish the spatial arrangement of Archaea, Crenarchaeota and Bacteria within biofilm architecture. Radioactive tracer experiments and micro-beta-imaging were used to describe substrate uptake patterns by members of the biofilm. The work represents a groundbrealking effort to investigate the role and in situ functionalism of Crenarchaeota and other groups within biotechnologically important granular biofilm-based ecosystems.