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Anaerobic and microaerophilic environments are pervasive in nature, providing essential contributions to the maintenance of human health, biogeochemical cycles and the Earth's climate. These ecological niches are characterised by low free oxygen and oxidants, or lack thereof. Under these conditions, interactions between species are essential for supporting the growth of syntrophic species and maintaining thermodynamic feasibility of anaerobic fermentation. Kinetic models provide a simplified view of complex metabolic networks, while genome-scale metabolic models and flux-balance analysis (FBA) aim to unravel these systems as a whole. The target of this review is to outline the main similarities, differences and challenges associated with kinetic and metabolic modelling, and describe state-of-the-art modelling practices for studying syntrophies in the anaerobic digestion (AD) case study. [Display omitted] • Anaerobic microbes play a significant role in the global biogeochemical cycle. • Mathematical models explain anaerobic processes, including bioconversion abilities, growth requirements and inhibitor susceptibility. • Kinetic modelling and FBA, are outlined, highlighting strengths and limitations. • The AD system is used as case of study to discuss modelling of syntrophies. [ABSTRACT FROM AUTHOR]