This chapter moves to the area for which Hierarchical Modelling of Species Communities (HMSC) is really meant, namely multi-species modelling. Thus, the chapter moves from univariate generalised linear mixed models to multivariate generalised linear mixed models, where the response variable is the vector of species occurrences or abundances. The chapter starts by discussing the difference between stacked species distribution modelling and joint species distribution modelling. It then builds HMSC as a joint species distribution model, first discussing how to model variation among species niches in general, and then adding hierarchical levels to specifically model species niches as a function of species’ traits, phylogenetic relationships or a combination of the two. The chapter illustrates joint species distribution modelling by applying the R-package HMSC-R first to simulated data and then to real data on a plant community.