We propose a novel Bayesian approach to modelling multimodal data generated by multiple independent processes, simultaneously solving the data association and induced supervised learning problems. Underpinning our approach is the use of Gaussian process priors which encode structure both on the functions and the associations themselves. The association of samples and functions are determined by taking both inputs and outputs into account while also obtaining a posterior belief about the relevance of the global components throughout the input space. We present an efficient learning scheme based on doubly stochastic variational inference and discuss how it can be applied to deep Gaussian process priors. We show results for an artificial data set, a noise separation problem, and a multimodal regression problem based on the cart-pole benchmark.