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Sky island species face climate-driven and anthropogenic habitat loss and population fragmentation, and are therefore vulnerable to genetic erosion. We conducted a genetic study of the cryptic and threatened alpine she-oak skink (Cyclodomorphus praealtus) throughout its range, across two regions of the mainland Australian Alps; an extensive high elevation plateau in the north (‘Kosciuszko Plateau’) and several smaller plateaus in the south (‘southern plateaus’). We investigated whether extensive potential habitat across Kosciuszko Plateau supported larger, connected populations with better genetic health than more fragmented southern plateaus. Our analyses of genome-wide markers confirmed effective isolation of the two regions. We identified three populations from the southern plateaus, largely aligning with discrete landforms, and four populations on Kosciuszko Plateau. Only one individual, from the …