Fibrillar aggregation of α-synuclein (αS) is a hallmark of Parkinson’s disease (PD) and related disorders, including multiple system atrophy (MSA) and dementia with Lewy bodies (DLB). Herein, the fibril interactions of two candidate positron emission tomography (PET) imaging ligands, M503 and HY-215, being developed for imaging of PD/DLB and MSA, respectively, are investigated. Photo-crosslinking mass spectrometry is used to determine the sites of their binding to in vitro fibrils, and Förster resonance energy transfer with fluorescently labeled proteins is used to analyze conformational changes in the disordered αS C-terminus. Taken together, these studies show that the MSA-selective PET lead, HY-215, interacts with the C-terminus, unlike the PD-selective lead M503. This study indicates that interactions with the often-ignored disordered regions of αS fibrils should be considered in the development of PET probes and other therapeutic small molecules.