Instability measurements of an axisymmetric, laminar separation bubble were made over a sharp cone-cylinder-flare with a
$12^{\circ }$
flare angle under hypersonic quiet flow. Two distinct instabilities were identified: Mack's second mode (which peaked between 190 and 290 kHz) and the shear-layer instability in the same frequency band as Mack's first mode (observed between 50 and 150 kHz). Both instabilities were measured with surface pressure sensors and were captured with high-speed schlieren. Linear stability analysis results agreed well with these measured instabilities in terms of both peak frequencies and amplification rates. Lower-frequency fluctuations were also noted in the schlieren data. Bicoherence analysis revealed nonlinear phase-locking between the shear-layer and second-mode instabilities. For the first time in axisymmetric, low-disturbance flow, naturally generated intermittent turbulent spots were observed in the reattached boundary layer. These spots appeared to evolve from shear-layer-instability wave packets convecting downstream. This work presents novel experimental evidence of the hypersonic shear-layer instability contributing directly to transition onset for an axisymmetric model.