Observations of the Lyman-alpha (Ly-$alpha$) forest may allow reionization to complete as late as $z sim 5.5$, provided the ionization state of the intergalactic medium (IGM) is sufficiently inhomogeneous at these redshifts. In this case, significantly neutral islands may remain amongst highly ionized gas with the ionized regions allowing some transmission through the Ly-$alpha$ forest. This possibility has the important virtue that it is eminently testable with existing Ly-$alpha$ forest data. In particular, we describe three observable signatures of significantly neutral gas in the $z sim 5.5$ IGM. We use mock quasar spectra produced from numerical simulations of reionization to develop these tests. First, we quantify how the abundance and length of absorbed regions in the forest increase with the volume-averaged neutral fraction in our reionization model. Second, we consider stacking the transmission profile around highly absorbed regions in the forest. If and only if there is significantly neutral gas in the IGM, absorption in the damping wing of the Ly-$alpha$ line will cause the transmission to recover slowly as one moves from absorbed to transmitted portions of the spectrum. Third, the deuterium Ly-$beta$ line should imprint a small but distinctive absorption feature slightly blueward of absorbed neutral regions in the Ly-$beta$ forest. We show that these tests can be carried out with existing Keck HIRES spectra at $z sim 5.5$, with the damping wing being observable for $< x_{text{HI}} >gtrsim 0.05$ and the deuterium feature observable with additional high-resolution spectra for $< x_{text{HI}} >gtrsim 0.2$.
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