The flavour structure of the general Two Higgs Doublet Model (2HDM) is analysed and a detailed study of the parameter space is presented, showing that flavour mixing in the 2HDM can be parametrized by various unitary matrices which arise from the misalignment in flavour space between pairs of various Hermitian flavour matrices which can be constructed within the model. This is entirely analogous to the generation of the CKM matrix in the Standard Model (SM). We construct weak basis invariants which can give insight into the physical implications of any flavour model, written in an arbitrary weak basis (WB) in the context of 2HDM. We apply this technique to two special cases, models with MFV and models with NNI structures. In both cases non-trivial CP-odd WB invariants arise in a mass power order much smaller than what one encounters in the SM, which can have important implications for baryogenesis in the framework of the general 2HDM.