Background: Synaptic degeneration is one of the pathological events in Alzheimer’s disease (AD), for which growth-associated protein 43 (GAP-43) and diffusion tensor imaging (DTI) could be an indicator. In this study, the CSF GAP-43 clinical trajectories and their association with progression and AD hallmarks with WM micro-structural alterations were evaluated. Methods: A total number of 133 participants were enrolled. GAP-43 and DTI values were compared between groups, both cross-sectionally and longitudinally. Subsequently, the potential of GAP-43 levels in the CSF in predicting DTI values was investigated using linear regression models.Result: CSF level of GAP-43 is negatively correlated with the mean diffusivity measures in Fornix (cres) / Stria terminalis in late and early MCI. Additionally, CSF level of GAP-43 is positively correlated with fractional anisotropy in cingulum in late MCI. Moreover, the Axial diffusivity in superior corona radiate and Radial diffusivity in superior fronto-occipital fasciculus (SFOF) was inversely correlated with GAP-43 level in the early and mid-MCI participants.Conclusion: Presynaptic marker GAP-43 in combination with DTI can be used as a novel biomarker to identify micro-structural synaptic degeneration in AD continuum; In addition, used as a specific and sensitive marker for tracking the progression of AD and monitoring potential micro-structural responses to treatments.