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Many non-migrating animals can perceive the Earth’s magnetic field, suggesting that magnetosensitivity may be a ubiquitous capacity that has been fine-tuned into a sense in migrating animals. A Cryptochrome (CRY)-based radical pair mechanism (RPM) provides a plausible pathway by which animals may sense magnetic fields. In the canonical model, the quantum spin state of a radical pair involving flavin adenine dinucleotide (FAD) and a series of Trp residues within CRY is sensitive to external magnetic fields that alter the ratio of activated to non-activated CRY. However, the 52-residue C-terminal fragment of Drosophila CRY (DmCRY), which lacks a canonical FAD binding pocket and the series of Trp residues, is sufficient to support magnetosensitivity, suggesting an additional/alternative reception mechanism. Here, we use all-atom molecular dynamic (MD) simulations to suggest that the C-terminus of Drosophila CRY (DmCRY-CT) may bind FAD via electrostatic interactions. This is supported by in vitro binding titrations that reveal a binding affinity in the nanomolar range and that FAD-binding drives the formation DmCRY-CT oligomers, reminiscent of CRY photobodiesobserved in plants. Mutating predicted key positively charged residues within the DmCRY-CT fragment to negatively charged ones disrupts binding both in silico and in vitro, and magnetosensitivity in both a circadian behavioural and a single neuron larval physiological assay in Drosophila. Our findings provide a plausible mechanistic basis for an alternative/additional CRY-FAD-mediated non-canonical RP mechanism for underlying magnetosensitivity in a tractable model organism.