This chapter discusses how Hierarchical Modelling of Species Communities (HMSC) can be used to model residual associations among species, with the aim of capturing biotic interactions. The chapter starts with an overview of the different modelling strategies that can be used for estimating biotic interactions in species distribution models. It then builds the statistical approach, first discussing the relationship between occurrence probabilities and co-occurrence probabilities and then describing how latent variables can be used to compactly model co-occurrences in species-rich communities. After introducing the baseline model, the chapter extends it to hierarchical, spatial and temporal study designs, as well as to cases where the biotic interactions depend on the environmental conditions. The chapter then focuses on interpretation, recalling that residual associations can be caused by many processes other than biotic interactions, therefore great caution must be taken when interpreting associations as biotic interactions. The chapter also discusses when and how the estimated species associations can be used to make improved predictions. The chapter finishes with two case studies, the first of which is based on simulated data and the second on sequencing data on dead-wood inhabiting fungi.