Over the last decade there has been a rapid development in culture-independent techniques for exploring microbial communities, which have led to new insights into their structure and function in both natural environments and engineered systems. This review focuses on some of the most important recent advances and their applications to the diverse microbial communities associated with anaerobic digestion. The use of these approaches in combination with complementary imaging techniques, chemical isotope analyses and detailed reactor performance measurements provides a new opportunity to develop a fundamental understanding of how microbial community dynamics, interactions and functionality influence digester efficiency and stability.