Seven human isoforms of importin α mediate nuclear import of cargo in a tissue- and isoform-specific manner. How nuclear import adaptors differentially interact with cargo harbouring the same nuclear localisation signal?(NLS) remains poorly understood， as the NLS recognition region is highly conserved. Here， we provide a structural basis for the nuclear import specificity of W proteins in Hendra and Nipah viruses. We determine the structural interfaces of these cargo bound to?importin α1 and α3， identifying a 2.4-fold more extensive interface and >?50-fold higher binding affinity for importin α3. Through the design of importin α1 and α3 chimeric and mutant proteins， together with structures of cargo-free importin α1 and α3 isoforms， we establish that the molecular basis of specificity resides in the differential positioning of the armadillo repeats 7 and 8. Overall， our study provides mechanistic insights into a range of important nucleocytoplasmic transport processes reliant on isoform adaptor specificity.