Microbial transformation of hydrocarbons to methane is an environmentally relevant but slow process taking place in a wide variety of electron acceptor-depleted environments, from oil reservoirs and coal deposits, to contaminated groundwater and deep sediments. Despite the prevalence of chemical evidence demonstrating methanogenic hydrocarbon metabolism in field investigations, there are significant gaps in our understanding of the anaerobic activation mechanisms of model substrates (particularly monoaromatic and polycyclic aromatic hydrocarbons, PAHs) and whole crude oil, as well as the degradation pathways and microorganisms governing oil transformation to methane. By studying the chemical and functional responses of methanogenic consortia to enrichment on model and mixed hydrocarbon substrates, we can gain a more complete understanding of the fate of hydrocarbon components in electron acceptor-depleted environments. In this dissertation, we sought to characterize the biodegradation of an expanded range of hydrocarbon substrates using a series of chemical and molecular approaches. We also explored cultivation-based strategies for optimizing rates of methanogenic hydrocarbon utilization, of which the most successful methods were adopted for future cultivation studies described here. Members of the Desulfosporosinus genus, known to catalyze methanogenic toluene biodegradation, were also found to co-metabolize other alkylbenzene substrates. Other members of the Firmicutes phylum, such as Desulfotomaculum, were shown to be functionally capable of activating toluene by addition to fumarate in a crude oil-degrading produced water consortium, and are proposed to play a key role in the formation of heavy oil in petroleum reservoirs. Microbial community sequencing, DNA-based stable isotope probing, and metagenomic surveys of previously established and novel methanogenic PAH-degrading cultures suggest that Clostridium may be important for degrading larger aromatic structures by an unknown mechanism. Experimental evidence of a hypothetical energy conservation mechanism in Syntrophus was detected during alkylbenzene biodegradation, suggesting this organism plays a vital role in coordinating syntrophic hydrocarbon biodegradation in a bioenergetically favourable manner. In all, this research has gleaned new insights into the microorganisms and metabolic processes regulating methanogenic hydrocarbon biodegradation, and has produced a wealth of new research questions to be explored in future investigations.