ABSTRACT: Abnormal protein phosphorylation is a fundamental trigger in the pathogenesis of Alzheimer’s Disease, leading to the formation of neurofibrillary tangles. Thus, molecular determination of the critical factors in controlling phosphorylation is desirable. Pin1, a cis-trans prolyl isomerase has recently been implicated in Alzheimer’s Disease progression. Moreover, Pin1 specifically targets phosphoproteins, regulating their function. Here, we reveal a novel interaction interface between Pin1 and the Collapsin Response Mediator Protein-2 (CRMP2); a protein found hyperphosphorylated alongside tau within neurofibrillary tangles. Using native mass spectrometry, we show that Pin1 binds to the disordered C-terminus of CRMP2 in a phosphorylation-dependent manner with residues Thr509 and Thr514 on CRMP2 important for enhanced binding affinity. Hydrogen-deuterium exchange mass spectrometry experiments further localized this binding site to the WW-domain of Pin1. Together, these findings provide novel insight into a putative regulatory role of Pin1 in modulating hyper-phosphorylation of CRMP2.